uniQure N.V. 10-K

Item 9A. Controls and Procedures . ​ Evaluation of Disclosure Controls and Procedures ​ Our management, with the participation of our chief executive officer (“CEO”, our principal executive officer) and chief financial officer (“CFO”, our principal financial officer), evaluated the effectiveness of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act) as of December 31, 2023. Based on such evaluation, our CEO and CFO have concluded that as of December 31, 2023, our disclosure controls and procedures were effective. 105 ​ Table of Contents ​ Management’s Annual Report on Internal Control Over Financial Reporting ​ Our management is responsible for establishing and maintaining adequate internal control over financial reporting, as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act. This rule defines internal control over financial reporting as a process designed by, or under the supervision of, a company’s chief executive officer and chief financial officer and effected by our board of directors, management and other personnel, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles and includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of our assets that could have a material effect on the financial statements. ​ We assessed the effectiveness of our internal control over financial reporting as of December 31, 2023. This assessment was performed under the direction and supervision of our CEO and CFO and based on criteria established in Internal Control - Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission (“COSO”). Our management’s assessment of the effectiveness of our internal control over financial reporting included testing and evaluating the design and operating effectiveness of our internal controls. In our management’s opinion, we have maintained effective internal control over financial reporting as of December 31, 2023, based on criteria established in the COSO 2013 framework. ​ Our independent registered public accounting firm, which has audited the consolidated financial statements included in this Annual Report on Form 10-K, has also issued an audit report on the effectiveness of our internal control over financial reporting as of December 31, 2023. Their report is filed within this Annual Report on Form 10-K. ​ Inherent Limitations of Internal Controls Our management, including our CEO and CFO, does not expect that our disclosure controls and procedures or our internal controls will prevent all errors and all fraud. A control system, no matter how well conceived and operated, can provide only reasonable, not absolute, assurance that the objectives of the control system are met. Because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that all control issues and instances of fraud, if any, within the Company have been detected. These inherent limitations include the realities that judgments in decision-making can be faulty, and that breakdowns can occur because of a simple error or mistake. Additionally, controls can be circumvented by the individual acts of some persons, by collusion of two or more people, or by management override of the control. The design of any system of controls also is based in part upon certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions. Over time, controls may become inadequate because of changes in conditions, or the degree of compliance with the policies or procedures may deteriorate. Projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements due to error or fraud. ​ Changes in internal control over financial reporting During the fourth quarter of 2023, there were no changes in our internal control over financial reporting (as defined in Rule 13a-15(f) under the Exchange Act) that materially affected, or are reasonably likely to materially affect, our internal control over financial reporting. ​ ​ ​ ​ ​ ​ ​ 106 ​ Table of Contents ​ Item 9B. Other Information ​ Trading Arrangements ​ During the three months ended December 31, 2023, none of our directors or officers informed us of the adoption , modification or termination of a “ Rule 10b5-1 trading arrangement ” or “ non-Rule 10b5-1 trading arrangement ,” as each term is defined in Item 408(a) of Regulation S-K. ​ Amendments to Code of Ethics ​ On February 27, 2024, our Board approved certain amendments to our Code of Business Conduct and Ethics (as amended, the “Code”) upon the recommendation of the Audit Committee of the Board. The Code was approved and adopted by the Board as part of its ordinary course and recurring review of our corporate codes and policies and applies to our employees, directors and officers. The amendments to the Code did not relate to or result in any waiver, explicit or implicit, of any provision of the Code in effect prior to the amendment. ​ The amendments to the Code update, clarify and, in certain cases, enhance provisions of the Code including, but not limited to, the reporting of actual or possible violations of the Code, the scope of matters that are reportable under the Code, the scope of the Audit Committee’s oversight regarding concerns and complaints involving allegations of fraud or violations of applicable law or regulation, and enforcement and compliance procedures with respect to alleged violations of the Code. ​ The above description of the Code does not purport to be complete and is qualified in its entirety by reference to the full text of the Code, a copy of which is filed as Exhibit 14.1 to this Annual Report on Form 10-K and available on the Investors & Media subpage of our website at www.uniqure.com under the “Corporate Governance” link. Information on our website shall not be deemed incorporated by reference into, or to be a part of, this Annual Report on Form 10-K. ​ ​ Item 9C. Disclosure Regarding Foreign Jurisdictions that Prevent Inspections ​ None. ​ Part III ​ Item 10. Directors, Executive Officers and Corporate Governance ​ The information required by this item is incorporated by reference from our Proxy Statement for our 2024 annual meeting of shareholders, which we will file within 120 days of December 31, 2023, or will be included in an amendment to this Annual Report on Form 10-K. ​ Item 11. Executive Compensation ​ The information required by this item is incorporated by reference from our Proxy Statement for our 2024 annual meeting of shareholders, which we will file within 120 days of December 31, 2023, or will be included in an amendment to this Annual Report on Form 10-K. ​ Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters ​ The information required by this item is incorporated by reference from our Proxy Statement for our 2024 annual meeting of shareholders, which we will file within 120 days of December 31, 2023, or will be included in an amendment to this Annual Report on Form 10-K. ​ Item 13. Certain Relationships and Related Transactions, and Director Independence ​ The information required by this item is incorporated by reference from our Proxy Statement for our 2024 annual meeting of shareholders, which we will file within 120 days of December 31, 2023, or will be included in an amendment to this Annual Report on Form 10-K. 107 ​ Table of Contents ​ Item 14. Principal Accounting Fees and Services ​ The information required by this item is incorporated by reference from our Proxy Statement for our 2024 annual meeting of shareholders, which we will file within 120 days of December 31, 2023, or will be included in an amendment to this Annual Report on Form 10-K. ​ ​ 108 ​ Table of Contents Part IV ​ Item 15. Exhibits, Financial Statements Schedules ​ Exhibits, Financial Statements Schedules ​ (a) Financial Statements . The following consolidated financial statements of uniQure N.V. are filed as part of this report: ​ ​ Page Report of Independent Registered Public Accounting Firm – KPMG Accountants N.V. 111 Consolidated Balance Sheets as of December 31, 2023 and 2022 113 Consolidated Statements of Operations and Comprehensive Loss for the Years Ended December 31, 2023, 2022 and 2021 114 Consolidated Statements of Shareholders’ Equity for the Years Ended December 31, 2023, 2022 and 2021 115 Consolidated Statements of Cash Flows for the Years Ended December 31, 2023, 2022 and 2021 116 Notes to Consolidated Financial Statements for the Years Ended December 31, 2023, 2022 and 2021 117 ​ (b) Financial Statements Schedules . Financial Statement Schedules have been omitted because of the absence of conditions under which they are required or because the required information, where material, is shown in the financial statements or notes. ​ (c) Other Exhibits . The Exhibit Index immediately preceding the signature page of this Annual Report on Form 10-K is incorporated herein by reference. ​ Item 16. Form 10-K Summary ​ Not applicable. ​ ​ 109 ​ Table of Contents ​ ​ INDEX TO CONSOLIDATED FINANCIAL STATEMENTS FOR THE YEARS ENDED DECEMBER 31, 2023, 2022 AND 2021 ​ ​ ​ Page Report of Independent Registered Public Accounting Firm - KPMG Accountants N.V. , Amstelveen, The Netherlands (PCAOB ID 1012 ) 111 Consolidated Balance Sheets as of December 31, 2023 and 2022 113 Consolidated Statements of Operations and Comprehensive Loss for the Years Ended December 31, 2023, 2022 and 2021 114 Consolidated Statements of Shareholders’ Equity for the Years Ended December 31, 2023, 2022 and 2021 115 Consolidated Statements of Cash Flows for the Years Ended December 31, 2023, 2022 and 2021 116 Notes to Consolidated Financial Statements 117 ​ ​ ​ 110 ​ Table of Contents Report of Independent Registered Public Accounting Firm ​ To the Shareholders and Board of Directors uniQure N.V.: ​ Opinions on the Consolidated Financial Statements and Internal Control Over Financial Reporting We have audited the accompanying consolidated balance sheets of uniQure N.V. and subsidiaries (the Company) as of December 31, 2023 and 2022, the related consolidated statements of operations and comprehensive loss, shareholders’ equity, and cash flows for each of the years in the three-year period ended December 31, 2023, and the related notes (collectively, the consolidated financial statements). We also have audited the Company’s internal control over financial reporting as of December 31, 2023, based on criteria established in Internal Control – Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission. In our opinion, the consolidated financial statements referred to above present fairly, in all material respects, the financial position of the Company as of December 31, 2023 and 2022, and the results of its operations and its cash flows for each of the years in the three year-period ended December 31, 2023, in conformity with U.S. generally accepted accounting principles. Also in our opinion, the Company maintained, in all material respects, effective internal control over financial reporting as of December 31, 2023 based on criteria established in Internal Control – Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission. Basis for Opinions The Company’s management is responsible for these consolidated financial statements, for maintaining effective internal control over financial reporting, and for its assessment of the effectiveness of internal control over financial reporting, included in the accompanying Management’s Annual Report on Internal Control Over Financial Reporting. Our responsibility is to express an opinion on the Company’s consolidated financial statements and an opinion on the Company’s internal control over financial reporting based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) (PCAOB) and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audits to obtain reasonable assurance about whether the consolidated financial statements are free of material misstatement, whether due to error or fraud, and whether effective internal control over financial reporting was maintained in all material respects. Our audits of the consolidated financial statements included performing procedures to assess the risks of material misstatement of the consolidated financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the consolidated financial statements. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the consolidated financial statements. Our audit of internal control over financial reporting included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, and testing and evaluating the design and operating effectiveness of internal control based on the assessed risk. Our audits also included performing such other procedures as we considered necessary in the circumstances. We believe that our audits provide a reasonable basis for our opinions. 111 ​ Table of Contents Definition and Limitations of Internal Control Over Financial Reporting A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements. Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. Critical Audit Matters Critical audit matters are matters arising from the current period audit of the consolidated financial statements that were communicated or required to be communicated to the audit committee and that: (1) relate to accounts or disclosures that are material to the consolidated f inancial statements and (2) involved our especially challenging, subjective, or complex judgments. We determined that there are no critical audit matters. ​ /s/ KPMG Accountants N.V. ​ We have served as the Company’s auditor since 2019. Amstelveen, the Netherlands February 28, 2024 ​ ​ ​ ​ ​ 112 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED BALANCE SHEETS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2023 2022 ​ ​ (in thousands, except share and per share amounts) Current assets ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 241,360 ​ $ 228,012 Current investment securities ​ ​ 376,532 ​ ​ 124,831 Accounts receivable and contract asset ​ ​ 4,193 ​ ​ 102,376 Inventories, net ​ ​ 12,024 ​ ​ 6,924 Prepaid expenses ​ ​ 15,089 ​ ​ 11,817 Other current assets and receivables ​ ​ 2,655 ​ ​ 2,814 Total current assets ​ ​ 651,853 ​ ​ 476,774 Non-current assets ​ ​ ​ ​ ​ ​ Property, plant and equipment, net ​ ​ 46,548 ​ ​ 50,532 Non-current investment securities ​ ​ — ​ ​ 39,984 Operating lease right-of-use assets ​ ​ 28,789 ​ ​ 32,726 Intangible assets, net ​ ​ 60,481 ​ ​ 58,778 Goodwill ​ ​ 26,379 ​ ​ 25,581 Deferred tax assets, net ​ ​ 12,276 ​ ​ 14,528 Other non-current assets ​ ​ 5,363 ​ ​ 6,061 Total non-current assets ​ ​ 179,836 ​ ​ 228,190 Total assets ​ $ 831,689 ​ $ 704,964 Current liabilities ​ ​ ​ ​ ​ ​ Accounts payable ​ $ 6,586 ​ $ 10,984 Accrued expenses and other current liabilities ​ ​ 30,534 ​ ​ 30,571 Current portion of contingent consideration ​ ​ 28,211 ​ ​ 25,982 Current portion of operating lease liabilities ​ ​ 8,344 ​ ​ 8,382 Total current liabilities ​ ​ 73,675 ​ ​ 75,919 Non-current liabilities ​ ​ ​ ​ ​ ​ Long-term debt ​ ​ 101,749 ​ ​ 102,791 Liability from royalty financing agreement ​ ​ 394,241 ​ ​ — Operating lease liabilities, net of current portion ​ ​ 28,316 ​ ​ 31,719 Contingent consideration, net of current portion ​ ​ 14,795 ​ ​ 9,334 Deferred tax liability, net ​ ​ 7,543 ​ ​ 8,257 Other non-current liabilities ​ ​ 3,700 ​ ​ 935 Total non-current liabilities ​ ​ 550,344 ​ ​ 153,036 Total liabilities ​ ​ 624,019 ​ ​ 228,955 Commitments and contingencies ​ ​ ​ ​ ​ ​ Shareholders' equity ​ ​ ​ ​ ​ ​ Ordinary shares, € 0.05 par value: 80,000,000 shares authorized as of December 31, 2023 and December 31, 2022 and 47,833,830 and 46,968,032 ordinary shares issued and outstanding as of December 31, 2023 and December 31, 2022, respectively ​ ​ 2,883 ​ ​ 2,838 Additional paid-in-capital ​ ​ 1,148,749 ​ ​ 1,113,393 Accumulated other comprehensive loss ​ ​ ( 53,553 ) ​ ​ ( 58,291 ) Accumulated deficit ​ ​ ( 890,409 ) ​ ​ ( 581,931 ) Total shareholders' equity ​ ​ 207,670 ​ ​ 476,009 Total liabilities and shareholders' equity ​ $ 831,689 ​ $ 704,964 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 113 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS AND INCOME ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2023 2022 ​ 2021 ​ ​ (in thousands, except share and per share amounts) License revenues ​ $ 2,758 ​ $ 100,000 ​ $ 517,400 Contract manufacturing revenues ​ ​ 10,835 ​ ​ 1,717 ​ ​ — Collaboration revenues ​ ​ 2,250 ​ ​ 4,766 ​ ​ 6,602 Total revenues ​ ​ 15,843 ​ ​ 106,483 ​ ​ 524,002 Operating expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cost of license revenues ​ ​ ( 65 ) ​ ​ ( 1,254 ) ​ ​ ( 24,976 ) Cost of contract manufacturing revenues ​ ​ ( 13,563 ) ​ ​ ( 2,089 ) ​ ​ — Research and development expenses ​ ​ ( 214,864 ) ​ ​ ( 197,591 ) ​ ​ ( 143,548 ) Selling, general and administrative expenses ​ ​ ( 74,591 ) ​ ​ ( 55,059 ) ​ ​ ( 56,290 ) Total operating expenses ​ ​ ( 303,083 ) ​ ​ ( 255,993 ) ​ ​ ( 224,814 ) Other income ​ ​ 6,059 ​ ​ 7,171 ​ ​ 12,306 Other expense ​ ​ ( 1,690 ) ​ ​ ( 820 ) ​ ​ ( 876 ) (Loss) / income from operations ​ ​ ( 282,871 ) ​ ​ ( 143,159 ) ​ ​ 310,618 Interest income ​ ​ 19,562 ​ ​ 609 ​ ​ 162 Interest expense ​ ​ ( 41,557 ) ​ ​ ( 11,704 ) ​ ​ ( 7,474 ) Foreign currency (losses) / gains, net ​ ​ ( 1,691 ) ​ ​ 23,235 ​ ​ 29,660 Other non-operating gains / (losses), net ​ ​ — ​ ​ 2,760 ​ ​ ( 160 ) (Loss) / income before income tax (expense) / benefit ​ $ ( 306,557 ) ​ $ ( 128,259 ) ​ $ 332,806 Income tax (expense) / benefit ​ ​ ( 1,921 ) ​ ​ 1,470 ​ ​ ( 3,217 ) Net (loss) / income ​ $ ( 308,478 ) ​ $ ( 126,789 ) ​ $ 329,589 Other comprehensive income / (loss): ​ ​ ​ ​ ​ ​ ​ ​ ​ Foreign currency translation gains / (losses), net ​ ​ 6,874 ​ ​ ( 29,435 ) ​ ​ ( 38,763 ) Defined benefit pension loss, net of taxes ​ ​ ( 2,136 ) ​ ​ — ​ ​ — Total comprehensive (loss) / income ​ $ ( 303,740 ) ​ $ ( 156,224 ) ​ $ 290,826 Earnings per ordinary share - basic ​ ​ ​ ​ ​ ​ ​ ​ ​ Basic net (loss) / income per ordinary share ​ $ ( 6.47 ) ​ $ ( 2.71 ) ​ $ 7.17 Earnings per ordinary share - diluted ​ ​ ​ ​ ​ ​ ​ ​ ​ Diluted net (loss) / income per ordinary share ​ $ ( 6.47 ) ​ $ ( 2.71 ) ​ $ 7.04 Weighted average shares - basic ​ ​ 47,670,986 ​ ​ 46,735,045 ​ ​ 45,986,467 Weighted average shares - diluted ​ ​ 47,670,986 ​ ​ 46,735,045 ​ ​ 46,840,972 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 114 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED STATEMENTS OF SHAREHOLDERS’ EQUITY ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ other ​ ​ ​ ​ Total ​ ​ Ordinary shares ​ paid-in ​ comprehensive ​ Accumulated ​ shareholders’ ​ ​ No. of shares Amount capital income / (loss) deficit equity ​ ​ (in thousands, except share and per share amounts) Balance at December 31, 2020 ​ 44,777,799 ​ $ 2,711 ​ $ 1,016,018 ​ $ 9,907 ​ $ ( 784,731 ) ​ $ 243,905 Income for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ 329,589 ​ ​ 329,589 Other comprehensive loss ​ — ​ ​ — ​ ​ — ​ ​ ( 38,763 ) ​ ​ — ​ ​ ( 38,763 ) Issuance of ordinary shares ​ 921,730 ​ ​ 55 ​ ​ 29,509 ​ ​ ​ ​ ​ ​ ​ ​ 29,564 Income tax benefit of past share issuance cost ​ ​ ​ ​ ​ ​ ​ 3,047 ​ ​ ​ ​ ​ ​ ​ ​ 3,047 Exercises of share options ​ 241,496 ​ ​ 15 ​ ​ 2,638 ​ ​ — ​ ​ — ​ ​ 2,653 Restricted and performance share units distributed during the period ​ 352,886 ​ ​ 21 ​ ​ ( 21 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 25,635 ​ ​ — ​ ​ — ​ ​ 25,635 Issuance of ordinary shares relating to employee stock purchase plan ​ 4,724 ​ ​ — ​ ​ 146 ​ ​ — ​ ​ — ​ ​ 146 Balance at December 31, 2021 ​ 46,298,635 ​ $ 2,802 ​ $ 1,076,972 ​ $ ( 28,856 ) ​ $ ( 455,142 ) ​ $ 595,776 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 126,789 ) ​ ​ ( 126,789 ) Other comprehensive loss ​ — ​ ​ — ​ ​ — ​ ​ ( 29,435 ) ​ ​ — ​ ​ ( 29,435 ) Income tax benefit of past share issuance cost ​ — ​ ​ — ​ ​ 808 ​ ​ — ​ ​ — ​ ​ 808 Exercises of share options ​ 152,356 ​ ​ 8 ​ ​ 1,272 ​ ​ — ​ ​ — ​ ​ 1,280 Restricted and performance share units distributed during the period ​ 505,799 ​ ​ 27 ​ ​ ( 27 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 34,204 ​ ​ — ​ ​ — ​ ​ 34,204 Issuance of ordinary shares relating to employee stock purchase plan ​ 11,242 ​ ​ 1 ​ ​ 164 ​ ​ — ​ ​ — ​ ​ 165 Balance at December 31, 2022 ​ 46,968,032 ​ $ 2,838 ​ $ 1,113,393 ​ $ ( 58,291 ) ​ $ ( 581,931 ) ​ $ 476,009 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 308,478 ) ​ ​ ( 308,478 ) Other comprehensive income, net ​ — ​ ​ — ​ ​ — ​ ​ 4,738 ​ ​ — ​ ​ 4,738 Exercises of share options ​ 14,070 ​ ​ 1 ​ ​ 129 ​ ​ — ​ ​ — ​ ​ 130 Restricted and performance share units distributed during the period ​ 832,530 ​ ​ 43 ​ ​ ( 43 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 35,093 ​ ​ — ​ ​ — ​ ​ 35,093 Issuance of ordinary shares relating to employee stock purchase plan ​ 19,198 ​ ​ 1 ​ ​ 177 ​ ​ — ​ ​ — ​ ​ 178 Balance at December 31, 2023 ​ 47,833,830 ​ $ 2,883 ​ $ 1,148,749 ​ $ ( 53,553 ) ​ $ ( 890,409 ) ​ $ 207,670 ​ The accompanying notes are an integral part of these consolidated financial statements ​ 115 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED STATEMENTS OF CASH FLOWS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2023 2022 2021 ​ ​ (in thousands) Cash flows from operating activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Net (loss) / income ​ $ ( 308,478 ) ​ $ ( 126,789 ) ​ $ 329,589 Adjustments to reconcile net (loss) / income to net cash (used in) / generated from operating activities: ​ ​ ​ ​ ​ ​ ​ ​ ​ Depreciation, amortization and impairment ​ ​ 11,900 ​ ​ 8,537 ​ ​ 7,299 Amortization of premium/discount on investment securities ​ ​ ( 10,917 ) ​ ​ - ​ ​ - Share-based compensation expense ​ ​ 35,093 ​ ​ 34,204 ​ ​ 25,635 Royalty financing agreement interest expense ​ ​ 26,933 ​ ​ - ​ ​ - Deferred tax expense / (income) ​ ​ 1,921 ​ ​ ( 1,470 ) ​ ​ 3,210 Changes in fair value of contingent consideration and derivative financial instrument, net ​ ​ 15,895 ​ ​ 4,320 ​ ​ 6,843 Unrealized foreign exchange gains, net ​ ​ ( 2,206 ) ​ ​ ( 22,083 ) ​ ​ ( 31,335 ) Other items, net ​ ​ 4,721 ​ ​ 1,605 ​ ​ ( 2,800 ) Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ Accounts receivable, prepaid expenses, and other current assets and receivables ​ ​ ( 1,323 ) ​ ​ ( 4,083 ) ​ ​ ( 3,959 ) Contract asset related to CSL Behring milestone payments ​ ​ 100,000 ​ ​ ( 45,000 ) ​ ​ ( 55,000 ) Inventories ​ ​ ( 6,740 ) ​ ​ ( 6,924 ) ​ ​ - Accounts payable ​ ​ ( 4,169 ) ​ ​ 9,238 ​ ​ ( 727 ) Accrued expenses, other liabilities, and operating leases ​ ​ ( 6,645 ) ​ ​ 3,385 ​ ​ 9,204 Contingent consideration milestone payment ​ ​ ( 1,914 ) ​ ​ - ​ ​ - Net cash (used in) / generated from operating activities ​ ​ ( 145,929 ) ​ ​ ( 145,060 ) ​ ​ 287,959 Cash flows from investing activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Investment in debt securities ​ ​ ( 366,439 ) ​ ​ ( 163,146 ) ​ ​ - Proceeds on maturity of debt securities ​ ​ 167,907 ​ ​ - ​ ​ - Purchases of property, plant, and equipment ​ ​ ( 7,154 ) ​ ​ ( 17,688 ) ​ ​ ( 17,438 ) Acquisition of uniQure France SAS, net of cash acquired ​ ​ - ​ ​ ( 1,900 ) ​ ​ ( 49,949 ) Net cash used in investing activities ​ ​ ( 205,686 ) ​ ​ ( 182,734 ) ​ ​ ( 67,387 ) Cash flows from financing activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Proceeds from issuance of ordinary shares ​ ​ - ​ ​ - ​ ​ 30,899 Share issuance costs from issuance of ordinary shares ​ ​ - ​ ​ - ​ ​ ( 1,334 ) Proceeds from royalty financing agreement ​ ​ 374,350 ​ ​ - ​ ​ - Payment of debt issuance costs ​ ​ ( 4,288 ) ​ ​ - ​ ​ - Repayment of debt acquired through acquisition of uniQure France SAS ​ ​ - ​ ​ - ​ ​ ( 1,572 ) Proceeds from loan increment, net of debt issuance costs ​ ​ - ​ ​ - ​ ​ 64,067 Proceeds from issuance of ordinary shares related to employee stock option and purchase plans ​ ​ 308 ​ ​ 1,445 ​ ​ 2,798 Contingent consideration milestone payment ​ ​ ( 7,649 ) ​ ​ - ​ ​ - Net cash generated from financing activities ​ ​ 362,721 ​ ​ 1,445 ​ ​ 94,858 Currency effect on cash, cash equivalents and restricted cash ​ ​ 2,265 ​ ​ ( 1,831 ) ​ ​ ( 3,757 ) Net increase / (decrease) in cash, cash equivalents and restricted cash ​ ​ 13,371 ​ ​ ( 328,180 ) ​ ​ 311,673 Cash, cash equivalents and restricted cash at beginning of period ​ ​ 231,173 ​ ​ 559,353 ​ ​ 247,680 Cash, cash equivalents and restricted cash at the end of period ​ $ 244,544 ​ $ 231,173 ​ $ 559,353 Cash and cash equivalents ​ $ 241,360 ​ $ 228,012 ​ $ 556,256 Restricted cash related to leasehold and other deposits ​ ​ 3,184 ​ ​ 3,161 ​ ​ 3,097 Total cash, cash equivalents and restricted cash ​ $ 244,544 ​ $ 231,173 ​ $ 559,353 Supplemental cash flow disclosures: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash paid for interest ​ $ ( 16,878 ) ​ $ ( 9,247 ) ​ $ ( 6,539 ) Non-cash decrease in accounts payables and accrued expenses and other current liabilities related to purchases of property, plant, and equipment ​ $ ( 513 ) ​ $ ( 964 ) ​ $ 1,488 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 116 ​ Table of Contents uniQure N.V. ​ NOTES TO CONSOLIDATED FINANCIAL STATEMENTS ​ 1. General business information ​ uniQure (the “Company”) was incorporated on January 9, 2012 as a private company with limited liability ( besloten vennootschap met beperkte aansprakelijkheid ) under the laws of the Netherlands. The Company is a leader in the field of gene therapy and seeks to deliver to patients suffering from rare and other devastating diseases single treatments with potentially curative results. The Company’s business was founded in 1998 and was initially operated through its predecessor company, Amsterdam Molecular Therapeutics Holding N.V (“AMT”). In 2012, AMT undertook a corporate reorganization, pursuant to which uniQure B.V. acquired the entire business and assets of AMT and completed a share-for-share exchange with the shareholders of AMT. Effective February 10, 2014, in connection with its initial public offering, the Company converted into a public company with limited liability ( naamloze vennootschap ) and changed its legal name from uniQure B.V. to uniQure N.V. ​ The Company is registered in the trade register of the Dutch Chamber of Commerce ( Kamer van Koophandel ) in Amsterdam, the Netherlands under number 54385229. The Company’s headquarters are in Amsterdam, the Netherlands, and its registered office is located at Paasheuvelweg 25, Amsterdam 1105 BP, the Netherlands and its telephone number is +31 20 240 6000. The Company’s website address is www.uniqure.com. ​ The Company’s ordinary shares are listed on the Nasdaq Global Select Market and trade under the symbol “QURE.” ​ 2. Summary of significant accounting policies ​ 2.1 Basis of preparation ​ The Company prepared its consolidated financial statements in compliance with generally accepted accounting principles in the United States (“U.S. GAAP”). Any reference in these notes to applicable guidance is meant to refer to authoritative U.S. GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Update (“ASU”) of the Financial Accounting Standards Board (“FASB”). ​ The consolidated financial statements have been prepared under the historical cost convention, except for derivative financial instruments and contingent consideration, which are recorded at fair value through profit or loss. ​ The consolidated financial statements are presented in United States (“U.S.”) dollars ($), except where otherwise indicated. Transactions denominated in currencies other than U.S. dollars are presented in the transaction currency with the U.S. dollar amount included in parenthesis, converted at the foreign exchange rate as of the transaction date. ​ The consolidated financial statements presented have been prepared on a going concern basis based on the Company’s cash and cash equivalents as of December 31, 2023 and the Company’s budgeted cash flows for the twelve months following the issuance date. ​ 2.2 Use of estimates ​ The preparation of consolidated financial statements, in conformity with U.S. GAAP and Securities and Exchange Commission (“SEC”) rules and regulations, requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosure of contingent assets and liabilities at the date of the consolidated financial statements and reported amounts of revenues and expenses during the reporting period. Estimates and assumptions are primarily made in relation to contingent consideration related to the acquisition of uniQure France SAS, the treatment of revenue to be recognized under the commercialization and license agreement entered into (“CSL Behring Agreement”) between the Company and CSL Behring LLC (“CSL Behring”), and the assessment of a valuation allowance on the Company’s deferred tax assets in the Netherlands. If actual results differ from the Company’s estimates, or to the extent these estimates are adjusted in future periods, the Company’s results of operations could either benefit from, or be adversely affected by, any such change in estimate. ​ 117 ​ Table of Contents 2.3 Accounting policies ​ The principal accounting policies applied in the preparation of these consolidated financial statements are set out below. These policies have been consistently applied to all the years presented, unless otherwise stated. ​ 2.3.1 Consolidation ​ The consolidated financial statements comprise the financial statements of the Company and its subsidiaries. Subsidiaries are all entities over which the Company has a controlling financial interest either through variable interest or through voting interest. Currently, the Company has no involvement with variable interest entities. ​ Inter-company transactions, balances, income, and expenses on transactions between uniQure entities are eliminated in consolidation. Profits and losses resulting from inter-company transactions that are recognized in assets are also eliminated. Accounting policies of subsidiaries have been changed where necessary to ensure consistency with the policies adopted by the Company. ​ 2.3.2 Current versus non-current classification ​ The Company presents assets and liabilities in the consolidated balance sheets based on current and non-current classification. ​ The term current assets is used to designate cash and other assets, or resources commonly identified as those that are reasonably expected to be realized in cash or sold or consumed during the normal operating cycle of the business. The Company’s normal operating cycle is twelve months . All other assets are classified as non-current. ​ The term current liabilities is used principally to designate obligations whose liquidation is reasonably expected to require the use of existing resources properly classifiable as current assets, or the creation of other current liabilities. Current liabilities are expected to be settled in the normal operating cycle. The Company classifies all other liabilities as non-current. ​ Deferred tax assets and liabilities are classified as non-current assets and liabilities, if any. ​ 2.3.3 Foreign currency translation ​ The functional currency of the Company and each of its entities (except for uniQure Inc. and Corlieve AG) is the euro (€). This represents the currency of the primary economic environment in which the entities operate. The functional currency of uniQure Inc. is the U.S. dollar ($) and the functional currency of Corlieve AG is the Swiss Franc (CHF). The consolidated financial statements are presented in U.S. dollars. ​ Foreign currency transactions are measured and recorded in the functional currency using the exchange rates prevailing at the dates of the transactions. Foreign exchange gains and losses resulting from the settlement of such transactions and from the re-measurement of monetary assets and liabilities denominated in foreign currencies at exchange rates prevailing at balance sheet date are recognized in profit and loss. ​ Upon consolidation, the assets and liabilities of foreign operations are translated into the functional currency of the shareholding entity at the exchange rates prevailing at the balance sheet date; items of income and expense are translated at monthly average exchange rates. The consolidated assets and liabilities are translated from uniQure N.V.’s functional currency, euro, into the reporting currency U.S. dollar at the exchange rates prevailing at the balance sheet date; items of income and expense are translated at monthly average exchange rates. Issued capital and additional paid-in capital are translated at historical rates with differences to the balance sheet date rate recorded as translation adjustments in other comprehensive income / loss. The exchange differences arising on translation for consolidation are recognized in “accumulated other comprehensive income / loss”. On disposal of a foreign operation, the component of other comprehensive income / loss relating to that foreign operation is recognized in profit or loss. ​ 118 ​ Table of Contents 2.3.4 Fair value measurement ​ The Company measures certain assets and liabilities at fair value, either upon initial recognition or for subsequent accounting or reporting. ASC 820, Fair Value Measurements and Disclosures requires disclosure of methodologies used in determining the reported fair values and establishes a hierarchy of inputs used when available. The three levels of the fair value hierarchy are described below: ​ ● Level 1 - Valuations based on unadjusted quoted prices in active markets for identical assets or liabilities that the Company can access at the measurement date. ​ ● Level 2 - Valuations based on quoted prices for similar assets or liabilities in markets that are not active or models for which the inputs are observable, either directly or indirectly. ​ ● Level 3 - Valuations that require inputs that reflect the Company’s own assumptions that are both significant to the fair value measurement and are unobservable. ​ To the extent that valuation is based on models or inputs that are less observable or unobservable in the market, the determination of fair value requires more judgment. Accordingly, the degree of judgment exercised by the Company in determining fair value is greatest for instruments categorized as Level 3. A financial instrument’s level within the fair value hierarchy is based on the lowest level of any input that is significant to the fair value measurement. ​ Items measured at fair value on a recurring basis include financial instruments and contingent consideration (Note 7, “ Fair value measurement ”). The carrying amount of cash and cash equivalents, accounts receivable from licensing and collaboration partners, other assets, accounts payable, accrued expenses and other current liabilities reflected in the consolidated balance sheets approximate their fair values due to their short-term maturities. ​ 2.3.5 uniQure France SAS transaction ​ On June 21, 2021, we entered into a share and purchase agreement (“SPA”) to acquire all of the outstanding ordinary shares of uniQure France SAS (formerly Corlieve Therapeutics SAS), a privately held French gene therapy company (“uniQure France SAS Transaction”). On July 30, 2021 (“Acquisition Date”), the Company acquired uniQure France SAS. The Company evaluated the uniQure France SAS transaction as to whether or not the transaction should be accounted for as a business combination or asset acquisition. Refer to Note 3 “ uniQure France SAS transaction ” for further detail. ​ a. Goodwill ​ Goodwill represents the excess of the fair value of the consideration transferred over the fair value of the net assets assumed in a business combination. Goodwill is not amortized but is evaluated for impairment on an annual basis and between annual tests if the Company becomes aware of any events occurring or changes in circumstances that would more likely than not reduce the fair value of the reporting unit below its carrying amount. As of December 31, 2023, 2022 and 2021, the Company has not recognized any impairment charges related to goodwill. ​ Refer to Note 3 “ uniQure France SAS transaction ” for further detail. ​ b. Acquired research and development ​ The Company identified various licenses that combined with the results of the research and development activities conducted in relation to its target candidate for the treatment of temporal lobe epilepsy (“AMT-260”) since incorporation of uniQure France SAS in 2019 constitute an In-process research and development intangible asset (“IPR&D Intangible Asset”). The IPR&D Intangible Asset is considered to be indefinite-lived until the completion or abandonment of the associated research and development efforts and is not amortized. If and when development is completed, which generally occurs when regulatory approval to market a product is obtained, the associated asset would be deemed finite-lived and would then be amortized based on its respective useful life at that point in time. For the years ended December 31, 2023, 2022 and 2021, the Company has not recognized any impairment charges related to the IPR&D Intangible Asset. 119 ​ Table of Contents In case of abandonment, the IPR&D Intangible Asset will be written-off. In accordance with ASC 350, Intangibles – Goodwill and Other, the Company tests indefinite-lived intangible assets for impairment on an annual basis and between annual tests if the Company becomes aware of any events occurring or changes in circumstances that would indicate the fair value of the IPR&D Intangible Asset is below its carrying amount. ​ Refer to Note 3 “ uniQure France SAS transaction ” for further detail. ​ c. Contingent consideration ​ Each reporting period, the Company revalues the contingent consideration obligations associated with the uniQure France SAS transaction to their fair value and records changes in the fair value within research and development expenses. Changes in contingent consideration obligations result from changes in assumptions regarding the probabilities of achieving the relevant milestones, or probability of success (“POS”), the estimated timing of achieving such milestones, and the interest rate to discount the payments. Payments of portions of contingent consideration initially recorded as of the acquisition date are recorded as cash flows from financing activities, and payments, or the portion of the milestone payments representing changes in the fair value of contingent consideration subsequent to the initial recognition are recorded as cash flows from operating activities. ​ Refer to Note 3 “ uniQure France SAS transaction ” for further detail. ​ 2.3.6 Notes to the consolidated statements of cash flows ​ The consolidated statements of cash flows have been prepared using the indirect method. The cash disclosed in the consolidated statements of cash flows is comprised of cash and cash equivalents and restricted cash. Cash and cash equivalents include bank balances, demand deposits and other short-term highly liquid investments (with maturities of less than three months at the time of purchase) that are readily convertible into a known amount of cash and are subject to an insignificant risk of fluctuation in value. ​ Cash flows denominated in foreign currencies have been translated at the average exchange rates. Exchange differences, if any, affecting cash and cash equivalents are shown separately in the consolidated statements of cash flows. Interest paid and received, and income taxes are included in net cash (used in) provided by operating activities. ​ 2.3.7 Segment information ​ Operating segments are identified as a component of an enterprise for which separate discrete financial information is available for evaluation by the chief operating decision maker, or decision-making group, in making decisions on how to allocate resources and assess performance. The Company views its operations and manages its business as one operating segment, which comprises the discovery, development, and commercialization of innovative gene therapies. ​ 2.3.8 Net (loss) / income per share ​ The Company follows the provisions of ASC 260, Earnings Per Share . In accordance with these provisions, net (loss) / income per share is calculated by dividing net (loss) / income by the weighted average number of ordinary shares outstanding during the period. ​ Diluted net (loss) / income per share reflects the dilution that would occur if share options or warrants to issue ordinary shares were exercised, performance or restricted share units were distributed, or shares under the employee share purchase plan were issued. However, potential ordinary shares are excluded if their effect is anti-dilutive. ​ Refer to Note 21 “ Basic and diluted earnings per share ” for further information. ​ 120 ​ Table of Contents 2.3.9 Impairment of long-lived assets ​ Long-lived assets, which include property, plant, and equipment and finite-lived intangible assets, are reviewed for impairment whenever events or changes in circumstances indicate that the carrying value of an asset or asset group may not be recoverable. Right-of-use assets are also reviewed for impairment in accordance with ASC 360, Property, Plant, and Equipment . The recoverability of the carrying value of an asset or asset group depends on the successful execution of the Company’s business initiatives and its ability to earn sufficient returns on approved products and product candidates. When such events or changes in circumstances occur, the Company assesses recoverability by determining whether the carrying value of such assets will be recovered through the undiscounted expected future cash flows. If the future undiscounted cash flows are less than the carrying amount of these assets, the Company recognizes an impairment loss based on the excess of the carrying value over the fair value of the assets. Fair value is determined through various valuation techniques, including discounted cash flow models, quoted market values, and third-party independent appraisals, as considered necessary. ​ Refer to Note 2.3.5 “ uniQure France SAS transaction ” for information on impairment testing related to goodwill and acquired research and development intangible assets. ​ 2.3.10 Investment securities ​ Investment securities consist of sovereign debt with residual maturities of less than 12 months (presented as current) and beyond (presented as non-current). The Company classifies these securities as held-to-maturity. Held-to-maturity securities are those securities in which the Company has the ability and intent to hold the security until maturity. Held-to-maturity securities are recorded at amortized cost, adjusted for applicable accrued interest and the amortization or accretion of premiums or discounts. Premiums and discounts are amortized or accreted over the term of the related held-to-maturity security as an adjustment to yield using the effective interest rate method. ​ Investments securities with original maturities of less than three months when purchased are presented within cash and cash equivalents (December 31, 2023: nil , December 31, 2022: $ 21.2 million). ​ A decline in the market value of any investment security below cost that is deemed to be other than temporary results in a reduction in the carrying amount to fair value. The impairment is charged to operations and a new cost base for the security is established. Other-than-temporary impairment charges are included in interest and other income (expense), net. Interest income is recognized when earned. ​ Refer to Note 6 “ Investment securities ” for further information. ​ 2.3.11 Accounts receivable ​ Accounts receivables include amounts due from services provided to the Company’s licensing and collaboration partners as well as unconditional rights to consideration from its licensing and collaboration partners. ​ 2.3.12 Inventories ​ The Company started producing commercial materials in April 2022 to supply CSL Behring in accordance with the June 2020 Development and Commercial Supply Agreement between the Company and CSL Behring. From this date onwards, the Company presents the costs associated with the aforementioned activities as cost of contract manufacturing. Refer to Note 5 “Collaboration arrangements and concentration of credit risk” for further detail. ​ Per ASC 330, Inventory, inventory is stated at the lower of cost or estimated net realizable value, on a first-in, first-out basis. The Company capitalizes raw materials to the extent these can be used in contract manufacturing for CSL Behring. The Company uses standard costs, approximating average costs to determine its cost basis for work in progress and finished goods. The Company’s assessment of recoverability value requires the use of estimates regarding the net realizable value of its inventory balances, including an assessment of excess or obsolete inventory. As applicable, write-downs resulting from adjustments to net realizable value will be recorded to cost of contract manufacturing. 121 ​ Table of Contents ​ 2.3.13 Prepaid expenses ​ Prepaid expenses are amounts paid in the period, for which the benefit has not been realized, and include payments made for insurance and research and clinical contracts. The related expense will be recognized in the subsequent period as incurred. ​ 2.3.14 Other (non) current assets ​ Deposits paid are either presented as other current assets or as other non-current assets based on duration of the underlying contractual arrangement. Deposits are classified as restricted cash and primarily relate to facility leases. ​ Contract assets are presented in current assets or as non-current assets based on the timing of the right to consideration. ​ 2.3.15 Property, plant, and equipment ​ Property, plant, and equipment is comprised mainly of laboratory equipment, leasehold improvements, construction-in-progress (“CIP”) and office equipment. All property, plant and equipment is stated at cost less accumulated depreciation. CIP consists of capitalized expenses associated with construction of assets not yet placed into service. Depreciation commences on CIP once the asset is placed into service based on its useful life determined at that time. ​ Maintenance and repairs that do not improve or extend the lives of the respective assets are expensed as incurred. Upon disposal, the related cost and accumulated depreciation is removed from the accounts and any resulting gain or loss on the transaction is recognized in the consolidated statements of operations and comprehensive loss. ​ Depreciation is calculated using the straight-line method over the estimated useful lives of the assets (or in the case of leasehold improvements a shorter lease term), which are as follows: ​ ​ ​ ​ ​ ​ ​ · Leasehold improvements Between 10 – 15 years · Laboratory equipment ​ 5 years · Office equipment ​ Between 3 – 5 years ​ 2.3.16 Leases ​ The Company records leases in accordance with ASC 842, Leases and determines if an arrangement is a lease at inception. Operating lease right-of-use assets and lease liabilities are initially recognized based on the present value of future minimum lease payments over the lease term at commencement date calculated using an incremental borrowing rate applicable to the lease asset unless the implicit rate is readily available. Lease terms may include options to extend or terminate the lease when it is reasonably certain that the Company will exercise that option. Leases with a term of twelve months or less are not recognized on the consolidated balance sheets. ​ The Company recognizes lease cost on a straight-line basis and presents these costs as operating expenses within the Consolidated statements of operations and comprehensive income / (loss). The Company presents lease payments within cash flows from operations within the Consolidated statements of cash flows. ​ 2.3.17 Accounts payable and accrued expenses ​ Accounts payables are invoiced amounts related to obligations to pay for goods or services that have been acquired in the ordinary course of business from suppliers. Accounts payables are recognized at the amounts invoiced by suppliers. ​ Accrued expenses are recognized for goods or services that have been acquired in the ordinary course of business. ​ Contract liabilities, if any, are presented in accrued expenses. 122 ​ Table of Contents 2.3.18 Long-term debt ​ Long-term debt is initially recognized at cost and presented net of original issue discount or premium and debt issuance costs on the consolidated balance sheets. Amortization of debt discount and debt issuance costs is recognized as interest expense in profit and loss over the period of the debt, using the effective interest rate method. ​ 2.3.19 Pensions and other post-retirement benefit plans ​ The Company has a defined contribution pension plan for all employees at its Amsterdam facility in the Netherlands, which is funded by the Company through payments to an insurance company, with individual accounts for each participants’ assets. The Company has no legal or constructive obligation to pay further contributions if the plan does not hold sufficient assets to pay all employees the benefits relating to services rendered in the current and prior periods. The contributions are expensed as incurred. Prepaid contributions are recognized as an asset to the extent that a cash refund or a reduction in the future payments is available. ​ In 2016, the Company adopted a qualified 401(k) Plan for all employees located in the United States. The 401(k) Plan offers both a pre-tax and post-tax (Roth) component. Employees may contribute up to the IRS statutory limit each calendar year. The Company matches $ 0.50 for every $ 1.00 contributed to the plan by participants up to 6 % of base compensation. Employer contributions are recognized as they are contributed, as long as the employee is rendering services in that period. If employer contributions are made in periods after an individual retires or terminates, the estimated cost is accrued during the employee’s service period. ​ The Company maintains defined benefit plans for its Swiss employees, including retirement benefit plans required by applicable local law. The Company accounts for pension assets and liabilities in accordance with ASC 715, Compensation - Retirement Benefits, which requires the recognition of the funded status of pension plans in the Company’s consolidated balance sheet. The liability in respect to defined benefit pension plans is the projected benefit obligation calculated annually by independent actuaries using the projected unit credit method. ​ The projected benefit obligation as of December 31, 2023 represents the actuarial present value of the estimated future payments required to settle the obligation that is attributable to employee services rendered before that date. Service cost is reported in research and development and general and administrative expenses. All other components of net period costs are reported in interest expense in the consolidated statement of operations and comprehensive loss. Plan assets are recorded at their fair value. Gains or losses arising from plan curtailments or settlements are accounted for at the time they occur. Actuarial gains and losses arising from differences between the actual and the expected return on plan assets are recognized in accumulated other comprehensive income (loss). ​ 2.3.20 Share-based compensation ​ The Company accounts for its share-based compensation awards in accordance with ASC 718, Compensation-Stock Compensation. ​ All the Company’s share-based compensation plans for employees are equity-classified. ASC 718 requires all share-based compensation to employees, including grants of employee options, restricted share units, performance share units and modifications to existing instruments, to be recognized in the consolidated statements of operations and comprehensive loss based on their grant-date fair values, net of an estimated forfeiture rate, over the requisite service period. Forfeitures of employee options are recognized as they occur. Compensation expense related to Performance Share Units is recognized when the Company considers achievement of the milestones to be probable. The requirements of ASC 718 are also applied to nonemployee share-based payment transactions except for specific guidance on certain inputs to an option-pricing model and the attribution of cost. ​ The Company uses a Hull & White option model to determine the fair value of option awards. The model captures early exercises by assuming that the likelihood of exercises will increase when the share-price reaches defined multiples of the strike price. This analysis is performed over the full contractual term. ​ ​ ​ 123 ​ Table of Contents 2.3.21 Revenue recognition ​ The Company primarily generates revenue from its commercialization and license agreement with CSL Behring. The Company generated revenue from services provided to Bristol-Myers Squibb (“BMS”) until February 21, 2023 (“Termination Date”). ​ CSL Behring collaboration ​ On June 24, 2020 (“Signing Date”), the Company entered into a commercialization and license agreement pursuant to which CSL Behring received exclusive global rights to etranacogene dezaparvovec (“Product”). On May 6, 2021, the CSL Behring Agreement became fully effective (“Closing”). The Company concluded that CSL Behring is a customer in accordance with ASC 606, Revenue from Contracts with Customers and identified two material performance obligations related to the CSL Behring Agreement: ​ (i) Sale of the exclusive global rights to etranacogene dezaparvovec, a gene therapy for patients with hemophilia B (the “Product”) (“License Sale”); and (ii) Generate information to support the regulatory approval of the current and next generation manufacturing process of the Product and to provide any such information generated to CSL Behring (“Manufacturing Development”). These performance obligations were considered distinct from one another, as CSL Behring can benefit from the identified service either on its own or together with other resources that are readily available to CSL Behring, and as the performance obligations are separately identifiable from other performance obligations in the CSL Behring Agreement. The Company continued to develop the Product between the Signing Date and Closing and performed certain reimbursable activities to fulfill the transfer of the global rights (“Additional Covenants” and together with the License the “License Sale”). The Additional Covenants are not considered distinct from the performance obligation to sell the license to CSL Behring as CSL Behring could not benefit from the Additional Covenants on their own, or have these activities be performed with readily available resources. ​ Refer to Note 5 “ Collaboration arrangements and concentration of credit risk ” for further detail. ​ Bristol-Myers Squib collaboration ​ The Company initially entered into collaboration, research, and license agreements with BMS in 2015 (“BMS CLA”) and amended them in 2020 (“amended BMS CLA”). The agreement terminated on February 21, 2023. ​ The Company provided pre-clinical research activities ("Collaboration Revenue") under the amended BMS CLA. ​ 2.3.22 Other income, other expense ​ The Company receives certain government and regional grants, which support its research efforts in defined projects, and include contributions towards the cost of research and development. These grants generally provide for reimbursement of approved costs incurred as defined in the respective grants and are deferred and recognized in the statements of operations and comprehensive loss over the period necessary to match them with the costs they are intended to compensate, when it is probable that the Company has complied with any conditions attached to the grant and will receive the reimbursement. ​ The Company’s other income also consists of employee retention credits received under the U.S. Coronavirus Aid, Relief, and Economic Security Act, income related to a settlement agreement that the Company and VectorY B.V. entered into in April 2021, as well as income from subleasing part of the Company’s Amsterdam facility. Other expense consists of expenses incurred in relation to the subleasing income. ​ ​ ​ ​ ​ 124 ​ Table of Contents 2.3.23 Research and development expenses ​ Research and development costs are expensed as incurred. Research and development expenses generally consist of laboratory research, clinical trials, statistical analysis, and report writing, regulatory compliance costs incurred with clinical research organizations and other third-party vendors (including post-approval commitments to conduct consistency and comparability studies). In addition, research and development expenses consist of start-up and validation costs related to the Company’s Lexington facility and the development and improvement of the Company’s manufacturing processes and methods. Furthermore, research and development costs include costs of materials and costs of intangible assets purchased from others for use in research and development activities. The costs of intangibles that are purchased from others for a particular research and development project and that have no alternative future uses (in other research and development projects or otherwise) are expensed as research and development costs at the time the costs are incurred or at the time when no alternative future use is identified. ​ 2.3.24 Income taxes ​ Income taxes are recorded in accordance with ASC 740, Income Taxes , which provides for deferred taxes using an asset and liability approach. The Company recognizes deferred tax assets and liabilities for the expected future tax consequences of events that have been included in the financial statements or tax returns. Deferred tax assets and liabilities are determined based on the difference between the financial statement carrying amount and the tax bases of assets and liabilities using enacted tax rates in effect for the year in which the differences are expected to reverse. Valuation allowances are provided, if based upon the weight of available evidence, it is more-likely-than-not that some or all the deferred tax assets will not be realized. ​ The benefits of tax positions are recognized only if those positions are more likely than not, based on the technical merits, to be sustained upon examination. Recognized tax positions are measured at the largest amount of tax benefit that is greater than 50 percent likely of being realized upon settlement. The determination as to whether the tax benefit will more-likely-than-not be realized is based upon the technical merits of the tax position as well as consideration of the available facts and circumstances. As of December 31, 2023, and 2022, the Company did not have any significant unrecognized tax benefits. ​ 2.3.25 Royalty Financing Agreement ​ In May 2023, uniQure biopharma B.V. (“uniQure biopharma”), a wholly-owned subsidiary of the Company entered into an agreement (the “Royalty Financing Agreement”) with the HemB SPV, L.P. (the “Purchaser”) to sell certain current and future royalties due to uniQure biopharma from CSL Behring under the CSL Behring Agreement by and between uniQure biopharma and CSL Behring from the net sales of HEMGENIX®. Refer to Note 14 “Royalty Financing Agreement” for further details of the Royalty Financing Agreement. The Company determined that the Royalty Financing Agreement should be accounted for as debt in accordance with topic ASC 470, Debt. The Company initially recognized the debt at fair value. The Company subsequently records the debt at amortized cost and determines the effective interest rate based on its projection of contractual cash flows. Interest expense (presented as “Interest Expense” in the consolidated statements of operations and comprehensive (loss) / income) is recorded over the projected repayment period using the effective interest method. The Company periodically assesses and adjusts the effective interest rate to reflect changes in projected cash flows. The Company prospectively applies the adjusted effective interest rate following the date of change. ​ In accordance with topic ASC 835, Interest, debt issuance costs incurred in relation to the Royalty Financing Agreement are presented as a reduction of carrying amount of the debt. Debt issuance cost is amortized together with the interest expense recorded. ​ 2.3.26 Restructuring expenses ​ Restructuring charges principally consist of one-time termination benefits. The Company records one-time termination benefits in accordance with ASC 420, Exit or Disposal Cost Obligations. One-time termination benefits are expensed at the date the Company notifies the employee, unless the employee must provide future service, in which case the benefits are expensed ratably over the future service period. ​ 125 ​ Table of Contents Other costs relate to the impairment of the Lexington facility that was closed as a result of a reorganization plan (the “Reorganization”). The Company has recognized an impairment loss of the right-of-use asset and corresponding leasehold improvements in accordance with ASC 360, Property, Plant and Equipment. ​ 2.3.27 Recently Adopted Accounting Pronouncements ​ None. ​ Recent Accounting Pronouncements Not Yet Effective ​ None. ​ ​ 3. uniQure France SAS transaction ​ At the Acquisition Date, the Company acquired uniQure France SAS (formerly Corlieve Therapeutics SAS). Following uniQure France SAS’s formation in November 2019, uniQure France SAS obtained exclusive licenses to certain patents from two French research institutions that continue to collaborate with the Company. uniQure France SAS also obtained an exclusive license from Regenxbio Inc. (“Regenxbio”). uniQure France SAS and Regenxbio simultaneously entered into a collaboration plan related to agreed joint preclinical research and development activities. At the Acquisition Date, uniQure France SAS and its Swiss subsidiary, Corlieve Therapeutics AG, employed seven employees. ​ The Company evaluated the uniQure France SAS transaction as to whether or not the transaction should be accounted for as a business combination or asset acquisition by first applying a screen test to determine if substantially all of the fair value of the gross assets acquired is concentrated in a single identifiable asset or group of similar identifiable assets. Based on the fair values of the gross assets acquired, the Company determined the screen test was not met. The Company further analyzed whether or not the acquired inputs and processes that have the ability to create outputs would meet the definition of a business. Significant judgment is required in the application of the screen test to determine whether an acquisition is a business combination or an acquisition of assets. ​ Identifiable assets and liabilities of uniQure France SAS, including identifiable intangible assets, were recorded at their fair values as of the Acquisition Date, when the Company obtained control. The excess of the fair value of the consideration transferred over the fair value of the net assets acquired was recorded as goodwill. ​ Consideration ​ On the Acquisition Date, the Company acquired 97.7 % of the outstanding ordinary shares of uniQure France SAS in return for EUR 44.9 million ($ 53.3 million as of the Acquisition Date). The Company acquired the remaining outstanding ordinary shares in February, July and September 2022 for a total of EUR 1.8 million ($ 1.9 million). ​ In addition to the payments to acquire 100 % of the outstanding ordinary shares, uniQure France SAS’s former shareholders are eligible to receive up to EUR 40.0 million ($ 44.1 million as of December 31, 2023) upon achievement of certain development milestones through Phase I/II, of which EUR 10.0 million ($ 10.6 million) was paid in September 2023, and EUR 160.0 million ($ 176.6 million as of December 31, 2023) upon achievement of certain milestones associated with Phase III development and obtaining approval to commercialize uniQure France SAS’s target candidate for the treatment of mesial temporal lobe epilepsy (“AMT-260” or “MTLE”) in the United States of America and the European Union. The Company may elect to pay up to 25 % of such milestone payments through the issuance of the Company’s ordinary shares. ​ As of the Acquisition Date, the Company recorded EUR 20.2 million ($ 24.0 million) as a contingent liability (presented as “Non-current liability”) for the fair value of these milestone payments. ​ Identified intangible assets ​ The Company identified various licenses that combined with the results of the research and development activities conducted in relation to AMT-260 since incorporation of uniQure France SAS in 2019 constitute an IPR&D Intangible Asset. 126 ​ Table of Contents ​ The Company determined the fair value of the IPR&D Intangible Asset using a present value model based on expected cash flows. Estimating the amounts and timing of cash flows required to complete the development of AMT-260 as well as net sales, cost of goods sold, and sales and marketing costs involved considerable judgment and uncertainty. The expected cash flows are materially impacted by the probability of successfully completing the various stages of development (i.e., dosing of first patient in clinical trial, advancing into late-stage clinical development and obtaining approval to commercialize a product candidate) as well as the weighted average cost of capital of 10.4 % used to discount the expected cash flows. Based on all such information and its judgment the Company estimated the fair value of the IPR&D Intangible Asset at EUR 53.6 million ($ 63.6 million) as of the Acquisition Date. ​ Deferred tax liability, net ​ uniQure France SAS’s deferred tax assets at the time of acquisition amounted to EUR 1.5 million ($ 1.7 million). Recognition of the IPR&D Intangible Asset gave rise to a deferred tax liability of EUR 13.4 million ($ 15.9 million) at the enacted French corporate income tax rate of 25.0 %. The Company consequently recorded a net deferred tax liability of EUR 11.9 million ($ 14.2 million as of the Acquisition Date). Changes in the net deferred tax liability after the Acquisition Date will be recorded in income tax expense in the Consolidated statements of operations and comprehensive income / (loss). ​ Goodwill ​ Goodwill represents the excess of total consideration over the estimated fair value of net assets acquired. The Company recorded EUR 23.9 million ($ 28.4 million) of goodwill in the consolidated balance sheet as of the Acquisition Date. The goodwill primarily relates to the recognition of a deferred tax liability recognized in association with the IPR&D Intangible asset of EUR 13.4 million ($ 15.9 million as of Acquisition Date) as well as the fair market value of the experienced workforce and potential synergies from the acquisition. The Company allocated the goodwill to its reporting unit. The Company does not expect any portion of this goodwill to be deductible for income tax purposes. ​ Debt As of the Acquisition Date, uniQure France SAS held a loan with outstanding amount equal to EUR 1.0 million ($ 1.2 million), which loan was repaid in its entirety in September 2021. As of the Acquisition Date, uniQure France SAS also held a loan with outstanding amount equal to EUR 0.4 million ($ 0.4 million), which was repaid in its entirety in December 2021. ​ Other As of the Acquisition Date, the Company also acquired other assets and assumed other liabilities, which included among others, EUR 2.9 million ($ 3.4 million) of current assets, which consisted of EUR 2.8 million ($ 3.3 million) of cash, and EUR 1.1 million ($ 1.3 million) of current liabilities. ​ 4. Reorganization ​ On October 5, 2023, the Company announced the Reorganization. As a result, the Company recorded severance and other personnel related expenses for the impacted employees. ​ In 2023, as a part of the Reorganization, the Company decided to sublease one of its laboratories in Lexington. The carrying amount of the right-of-use asset was determined not to be recoverable. As a result, the Company recorded impairment charges for the related operating lease right-of-use assets and leasehold improvements. ​ ​ ​ ​ 127 ​ Table of Contents A summary of the restructuring charges for the year ended December 31, 2023 by major activity type is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ Severance and Other Personnel Costs Impairment Charges Total ​ ​ ​ (in thousands) Research and development ​ $ 2,188 1,438 3,626 General and administrative ​ ​ 361 — 361 Total ​ $ 2,549 1,438 3,987 ​ A summary of the changes in the severance and other personnel liabilities, included within accrued expenses and other current liabilities on the consolidated balance sheets, related to the workforce reduction is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amount of liability ​ ​ ​ (in thousands) Balance as of January 1, 2023 ​ $ — Severance and other personnel costs ​ ​ 2,549 Cash payments during the period ​ ​ ( 1,522 ) Balance as of December 31, 2023 ​ $ 1,027 ​ ​ ​ ​ 5. Collaboration arrangements and concentration of credit risk ​ CSL Behring collaboration ​ License Sale The Company determined that the fixed upfront payment of $ 450.0 million and the $ 12.4 million that the Company received in May 2021 in relation to the Additional Covenants should be allocated to the License Sale. In addition, the Company concluded that variable milestone payments, sales milestone payments and royalties should be allocated to the License Sale performance obligation as well. The Company determined that the License Sale was completed on May 6, 2021, when it transferred the license and CSL Behring assumed full responsibility for the development and commercialization of the Product. At Closing, the Company evaluated the amounts of potential payments and the likelihood that the payments will be received. The Company utilized the most likely amount method to estimate the variable consideration to be included in the transaction price. Since the Company cannot control the achievement of regulatory and first commercial sales milestones, the Company concluded that the potential payments were constrained as of Closing. The Company determined that it would recognize revenue related to these payments only to the extent that it becomes probable that no significant reversal of recognized cumulative revenue will occur thereafter. The Company determined that achievement of a total of $ 55.0 million of milestone payments related to the submissions of a biologics license application (“BLA”) and market authorization application (“MAA”) was probable as of February 25, 2022, the time of filing the 2021 financial statements, and hence recorded these as license revenue in the year ended December 31, 2021. In March and April 2022, the global regulatory submissions were submitted, and the Company received the $ 55.0 million owed to it from CSL Behring. The Company recorded $ 100.0 million in variable milestone revenue related to a first sale of HEMGENIX ® in the U.S. during the year ended December 31, 2022 as the Company considered the occurrence of this event to be probable following the November 2022 BLA approval of HEMGENIX ® . The Company collected the $ 100.0 million payment from CSL Behring in July 2023 following the first sale of the Product in the U.S in June 2023. The Company is also eligible to receive up to $ 1.3 billion in additional payments based on the achievement of commercial milestones, which are not subject to the Royalty Financing Agreement. Royalties on the sale of HEMGENIX® are recorded once earned and are presented as license revenue. ​ 128 ​ Table of Contents The Company recognized $ 2.8 million (of which all related to royalty revenue), $ 100.0 million ( nil related to royalty revenue) and $ 517.4 million ( nil related to royalty revenue) of revenues related to the License Sale in the years ended December 31, 2023, 2022 and 2021, respectively. ​ The Company recorded expenses related to its existing license and other agreements as well as its financial advisor for a high single digit percentage of any such revenue recognized associated to meeting a milestone. Manufacturing Development ​ The Company determined that a $ 50.0 million variable milestone payment related to Manufacturing Development should be allocated to the Manufacturing Development performance obligation. The Company concluded that this milestone payment represents the stand-alone selling price (“SSP”) of the services based on the estimated cost of providing the services including a reasonable margin. Manufacturing Development includes providing information regarding a next generation manufacturing process of the Product to CSL Behring. CSL Behring did not request such services during the year ended December 31, 2023. The variable consideration will be reduced based on a formula linked to quantities supplied using the currently approved manufacturing process following the one year anniversaries of the BLA and MAA approvals. In conjunction with the ongoing technology transfer (see below), the Company is not actively generating information with respect to a next generation manufacturing process of the Product. The Company utilized the most likely amount method to estimate the variable consideration to be included in the transaction price. As of December 31, 2023, the Company has not recognized any revenue related to the Manufacturing Development milestone. Contract manufacturing ​ On the Signing Date, the Company and CSL Behring entered into a development and commercial supply agreement, pursuant to which, among other things, the Company will supply HEMGENIX ® to CSL Behring at an agreed-upon price commensurate with the SSP. The Company will be responsible for supplying development and commercial Product until such time that these capabilities may be transferred to CSL Behring or a designated contract manufacturing organization. On September 6, 2022, CSL Behring notified the Company of its intent to transfer manufacturing technology related to the Product in the coming years to a third-party contract manufacturer designated by CSL Behring. The Company generated $ 10.8 million, $ 1.7 million and nil contract manufacturing revenue from sales to CSL Behring during the years ended December 31, 2023, 2022 and 2021. The Company recognizes contract manufacturing revenue when CSL Behring obtains control of HEMGENIX ®. The Company incurred $ 13.6 million, $ 2.1 million and nil of cost in relation to its contract manufacturing activities during the years ended December 31, 2023, 2022 and 2021. Collaboration services ​ Following Closing, the Company was facilitating the completion of the HOPE-B clinical trial on behalf of CSL Behring until CSL Behring took over the execution of the clinical trials in December 2022. Activities related to on-demand development services and other services in accordance with the CSL Behring Agreement as well as activities related to the completing the HOPE-B clinical trial are reimbursed by CSL Behring at an agreed full-time-employee rate (“FTE-rate”) and CSL Behring also reimbursed agreed third-party expenses incurred in relation to performing these activities. The Company concluded that these rights at Closing did not represent material rights. The Company recognized $ 2.3 million of collaboration revenue in the year ended December 31, 2023, compared to $ 3.0 million and $ 2.4 million in the same periods in 2022 and 2021. Accounts r eceivable and c ontract asset As of December 31, 2023, the Company recorded accounts receivable of $ 4.0 million from CSL Behring related to collaboration services, contract manufacturing revenue and royalty revenue. As of December 31, 2022, the Company recorded accounts receivable of $ 2.2 million from CSL Behring related to collaboration services as well as a contract asset of $ 100.0 million for a milestone due from CSL Behring following the first sale of HEMGENIX ® in the U.S., which was collected in July 2023. 129 ​ Table of Contents As of December 31, 2021, the Company recorded accounts receivable of $ 2.9 million from CSL Behring related to collaboration services as well as a contract asset of $ 55.0 million associated with milestone payments due upon CSL Behring’s global regulatory submissions for HEMGENIX™ which were collected in March and April 2022. Bristol-Myers Squibb collaboration ​ On November 21, 2022, the Company received written notice that BMS is terminating the BMS CLA as amended effective February 21, 2023. ​ The Company recognized collaboration revenues associated with Collaboration Target-specific pre-clinical analytical development and process development activities that were reimbursable by BMS under the amended BMS CLA as well as other related agreements. Collaboration revenue related to these contracted services was recognized when performance obligations were satisfied. Total collaboration revenue generated with BMS are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2023 ​ ​ 2022 ​ ​ 2021 ​ ​ (in thousands) Bristol Myers Squibb $ — ​ $ 1,752 ​ $ 4,176 ​ $ — ​ $ 1,752 ​ $ 4,176 ​ ​ Amounts owed by BMS in relation to the collaboration revenue are as follows (presented as “Accounts receivable”) as of December 31, 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2023 2022 ​ ​ (in thousands) Bristol Myers Squibb ​ $ — ​ $ 136 Total ​ $ — ​ $ 136 ​ ​ 6. Investments securities ​ The following table summarizes the Company’s investments into sovereign debt as of December 31, 2023 and 2022: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At December 31, 2023 ​ ​ Amortized cost ​ Gross unrealized holding gains ​ Gross unrealized holding losses ​ Estimated fair value ​ ​ (in thousands) Current investments: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Government debt securities (held-to-maturity) ​ $ 376,532 ​ $ 139 ​ $ — ​ $ 376,671 Total ​ $ 376,532 ​ $ 139 ​ $ — ​ $ 376,671 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At December 31, 2022 ​ ​ Amortized cost ​ Gross unrealized holding gains ​ Gross unrealized holding losses ​ Estimated fair value ​ ​ (in thousands) Current investments: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Government debt securities (held-to-maturity) ​ $ 124,831 ​ $ — ​ $ ( 283 ) ​ $ 124,548 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Non-current investments: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Government debt securities (held-to-maturity) ​ ​ 39,984 ​ ​ — ​ ​ ( 43 ) ​ ​ 39,941 Total ​ $ 164,815 ​ $ — ​ $ ( 326 ) ​ $ 164,489 ​ 130 ​ Table of Contents The Company invests in short-term U.S. and European government bonds with the highest investment credit rating. The U.S. and European government bonds are U.S. dollar and euro denominated, respectively. Inputs to the fair value of the investments are considered Level 2 inputs. ​ 7. Inventories ​ The following table summarizes the inventory balances, net of reserves, as of December 31, 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2023 2022 ​ ​ (in thousands) Raw materials ​ $ 7,157 ​ $ 3,584 Work in progress ​ ​ 4,109 ​ ​ 1,874 Finished goods ​ ​ 758 ​ ​ 1,466 Inventories ​ $ 12,024 ​ $ 6,924 ​ The Company recorded write downs of $ 1.6 million and nil for the years ended December 31, 2023 and December 31, 2022. The costs are recognized as Cost of Contract Manufacturing Revenues. ​ ​ ​ 8. Fair value measurement and Other non-operating (losses) / gains ​ The Company measures certain financial assets and liabilities at fair value, either upon initial recognition or for subsequent accounting or reporting. ​ The carrying amount of cash and cash equivalents, accounts receivable from licensing and collaboration partners, other assets, accounts payable, accrued expenses and other current liabilities reflected in the consolidated balance sheets approximate their fair values due to their short-term maturities. ​ The Company’s material financial assets include cash and cash equivalents, restricted cash and investment securities. Cash and cash equivalents and restricted cash are measured at fair value using Level 1 inputs. Restricted cash is included within “Other non-current assets” within the consolidated balance sheets. Investment securities are measured at amortized cost. ​ The following table sets forth the balances and changes in fair values of liabilities that are measured at fair value using Level 3 inputs: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Derivative ​ ​ ​ ​ ​ Contingent ​ financial ​ ​ ​ ​ consideration instruments Total ​ ​ (in thousands) Balance at December 31, 2020 ​ $ — ​ $ 2,645 ​ $ 2,645 Amount recorded for contingent consideration on Acquisition Date of uniQure France SAS ​ ​ 23,950 ​ ​ — ​ ​ 23,950 Net losses recognized in profit or loss ​ ​ 6,683 ​ ​ 160 ​ ​ 6,843 Currency translation effects ​ ​ ( 1,091 ) ​ ​ — ​ ​ ( 1,091 ) Balance at December 31, 2021 ​ $ 29,542 ​ $ 2,805 ​ $ 32,347 Net losses / (gains) recognized in profit or loss ​ ​ 7,080 ​ ​ ( 2,760 ) ​ ​ 4,320 Currency translation effects ​ ​ ( 1,306 ) ​ ​ ( 45 ) ​ ​ ( 1,351 ) Balance at December 31, 2022 ​ $ 35,316 ​ $ — ​ $ 35,316 Net losses recognized in profit or loss ​ ​ 15,895 ​ ​ — ​ ​ 15,895 Contingent consideration milestone payment ​ ​ ( 9,563 ) ​ ​ — ​ ​ ( 9,563 ) Currency translation effects ​ ​ 1,358 ​ ​ — ​ ​ 1,358 Balance at December 31, 2023 ​ $ 43,006 ​ $ — ​ $ 43,006 ​ 131 ​ Table of Contents Contingent consideration ​ The Company is required to pay up to EUR 178.8 million ($ 197.3 million at the December 31, 2023 foreign exchange rate) to the former shareholders of uniQure France SAS (formerly Corlieve Therapeutics SAS) upon the achievement of contractually defined milestones in connection with the Company’s acquisition of uniQure France (refer to Note 3 “uniQure France SAS transaction” ). The Company recorded a liability for the fair market value of the contingent consideration of EUR 20.2 million ($ 24.0 million) at the Acquisition Date. The fair market value was determined using unobservable initial inputs with respect to (i) the probability of achieving the relevant milestones, or POS, (ii) the estimated timing of achieving such milestones, and (iii) the interest rate used to discount the payments. The Company determined the fair market value of the contingent consideration by calculating the probability-adjusted payments based on each milestone’s probability of achievement. The probability-adjusted payments were then discounted to present value using a discount rate representing the Company’s credit risk. This discount rate was determined using the effective interest rate of the Company’s existing debt facility adjusted for difference in maturity dates based on market data on effective yields for U.S. bonds with a CCC credit rating. In September 2023, a milestone payment of EUR 10.0 million ($ 10.6 million) was paid, of which EUR 8.9 million ($ 9.6 million) related to contingent consideration. ​ The fair value of the contingent consideration as of December 31, 2023 was $ 43.0 million (December 31, 2022: $ 35.3 million) using discount rates of approximately 15.3 % to 15.6 % (December 31, 2022: 14.0 % to 14.4 %). Following the clearance of an Investigational New Drug (“IND”) application for AMT-260 in August 2023, the Company increased the probability of achieving a EUR 30.0 million ($ 33.1 million) milestone payment following the dosing of the first patient in Phase I/II clinical trial from 66.0 % to 100.0 %. This also resulted in an increase of the probability that AMT-260 may advance to late-stage development and commercialization. ​ If as of December 31, 2023 the Company had assumed a 100 % likelihood of AMT-260 advancing into a Phase III clinical study, then the fair value of the contingent consideration would have increased to $ 75.9 million. If as of December 31, 2023 the Company had assumed that it would discontinue development of the AMT-260 program, then the contingent consideration would have been released to income. ​ As of December 31, 2023, the Company classified $ 28.2 million of the total contingent consideration of $ 43.0 million as current liabilities. The balance sheet classification between current and non-current liabilities is based upon the Company’s best estimate of the timing of settlement of the remaining relevant milestones. ​ Derivative financial instruments ​ The Company recorded the following results in other non-operating (losses) / gains related to the changes in the fair value of derivative financial instruments. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ 2023 ​ 2022 ​ 2021 ​ ​ (in thousands) Other non-operating gains: ​ ​ ​ ​ ​ ​ ​ ​ ​ Derivative gains ​ $ — ​ $ 2,760 ​ $ — Total other non-operating gains: ​ ​ — ​ ​ 2,760 ​ ​ — Other non-operating losses: ​ ​ ​ ​ ​ ​ ​ ​ ​ Derivative losses ​ ​ — ​ ​ — ​ ​ ( 160 ) Other non-operating gains / (losses), net ​ $ — ​ $ 2,760 ​ $ ( 160 ) ​ Derivative financial instruments BMS ​ On December 1, 2020, as part of the amended BMS CLA, the Company and BMS agreed that upon the consummation of a change of control transaction of uniQure that occurs prior to December 1, 2026 or BMS’ delivery of a target cessation notice for all four Collaboration Targets, the Company (or its third party acquirer) shall pay to BMS a one-time, non-refundable, non-creditable cash payment of $ 70.0 million, provided that (x) if $ 70.0 million is greater than five percent ( 5.0 %) of the net proceeds (as contractually defined) from such change of control transaction, the payment shall be an amount equal to five percent of such net proceeds, and (y) if $ 70.0 million is less than one percent of such net proceeds, the change of control payment shall be an amount equal to one percent of such net proceeds (“CoC-payment”). The amended BMS CLA was terminated on February 21, 2023. 132 ​ Table of Contents The Company had previously determined that the CoC-payment should be recorded as a derivative financial liability as of the December 1, 2020 initial recognition and that subsequent changes in the fair market value of this derivative financial liability should be recorded in profit and loss. ​ The Company determined the fair market value of the derivative financial liability to be nil as of December 31, 2022 as no change of control transaction had been consummated prior to the termination of the amended BMS CLA on February 21, 2023. This resulted in the derecognition of the derivative financial liability for the year ended December 31, 2022. ​ Accordingly, the Company recorded a $ 2.8 million gain within “Other non-operating (losses) / gains” in the year ended December 31, 2022 and no such gains or losses were recorded in the year ended December 31, 2023. ​ Other ​ As of December 31, 2023, the Company recorded $ 0.5 million liability related to consideration for post-acquisition services, presented within Other non-current liabilities in connection with the Company’s acquisition of uniQure France SAS (December 31, 2022: $ 0.3 million). ​ Investment securities ​ Refer to Note 6 “ Investment securities ” for the fair value of the investment securities as of December 31, 2023. ​ Pension plan assets ​ Refer to Note 15 “ Retirement benefits ” for the fair value of the plan assets as of December 31, 2023. ​ ​ Other ​ ​ ​ 9. Property, plant, and equipment, net ​ The following table presents the Company’s property, plant, and equipment as of December 31: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2023 2022 ​ ​ (in thousands) Leasehold improvements ​ $ 46,512 ​ $ 44,871 Laboratory equipment ​ ​ 43,657 ​ ​ 39,393 Office equipment ​ ​ 6,383 ​ ​ 4,985 Construction-in-progress ​ ​ 5,668 ​ ​ 5,409 Total property, plant, and equipment ​ ​ 102,220 ​ ​ 94,658 Less accumulated depreciation ​ ​ ( 55,672 ) ​ ​ ( 44,126 ) Property, plant and equipment, net ​ $ 46,548 ​ $ 50,532 ​ Total depreciation expense was $ 10.3 million for the year ended December 31, 2023 (December 31, 2022: $ 8.2 million, December 31, 2021: $ 6.1 million). Depreciation expense is allocated to research and development expenses and cost of contract manufacturing to the extent it relates to the Company’s manufacturing facility and equipment and laboratory equipment. All other depreciation expenses are allocated to selling, general and administrative expense. ​ The following table summarizes property, plant, and equipment by geographic region. ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, December 31, ​ ​ 2023 ​ 2022 ​ ​ (in thousands) Lexington, Massachusetts (United States of America) ​ $ 19,437 ​ $ 20,258 Amsterdam (the Netherlands) ​ 27,095 ​ 30,252 Other ​ ​ 16 ​ ​ 22 Total ​ $ 46,548 ​ $ 50,532 ​ 133 ​ Table of Contents ​ 10. Right-of-use asset and lease liabilities ​ The Company’s most significant leases relate to office and laboratory space under the following operating lease agreements: ​ Lexington, Massachusetts / United States ​ In July 2013, the Company entered into a lease for a facility in Lexington, Massachusetts, United States. The term of the lease commenced in November 2013, was set for 10 years starting from the 2014 rent commencement date and is non-cancellable. Originally, the lease for this facility had a termination date of 2024. In November 2018, the term was expanded by five years to June 2029. The lease continues to be renewable for two subsequent five-year terms. Additionally, the lease was expanded to include an additional 30,655 square feet within the same facility and for the same term. The lease of the expansion space commenced on June 1, 2019. ​ The contractually fixed annual increase of lease payments through 2029 for both the extension and expansion lease have been included in the lease payments. ​ In December 2021, the Company entered into a new lease for an additional facility in Lexington, Massachusetts, United States of approximately 13,501 square feet of space. The lease commenced in May 2022. Following the Company’s announcement of the Reorganization, the Company incurred costs amounting to $ 1.4 million associated with the impairment of the right-of-use asset and its associated leasehold improvements’ carrying value that was determined not be recoverable as of the cease-use date in late 2023. This facility is intended to be subleased in 2024. In February 2022, the Company also entered into a new lease for an additional facility in Lexington, Massachusetts, United States of approximately 12,716 square feet. The lease commenced in November 2022 and is set for a non-cancellable period of seven years and four months . The lease is renewable for one five-year term. Amsterdam / The Netherlands ​ In March 2016, the Company entered into a 16-year lease for a facility in Amsterdam, the Netherlands and amended this agreement in June 2016. The lease for the facility terminates in 2032, with an option to extend in increments of five-year periods. The lease contract includes variable lease payments related to annual increases in payments based on a consumer price index. ​ On December 1, 2017, the Company entered into an agreement to sub-lease three of the seven floors of its Amsterdam facility for a ten-year term ending on December 31, 2027, with an option for the sub-lessee to extend until December 31, 2031. In February 2020, the Company amended the agreement to sub-lease to take back one of the three floors effective March 1, 2020. The fixed lease payments to be received during the remaining term under the agreement to sub-lease amount to EUR 3.6 million ($ 4.0 million) as of December 31, 2023. ​ In May 2021, the Company entered into a sublease agreement to let an additional approximately 1,080 square meters of office space to accommodate the hiring of additional full-time employees. The lease expires in October 2028. ​ 134 ​ Table of Contents Operating lease liabilities ​ The components of lease cost were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2023 2022 2021 ​ ​ (in thousands) ​ ​ ​ Operating lease cost ​ $ 7,018 ​ $ 5,932 ​ $ 5,306 Variable lease cost ​ ​ 1,238 ​ ​ 785 ​ ​ 698 Sublease income ​ ​ ( 957 ) ​ ​ ( 849 ) ​ ​ ( 907 ) Total lease cost ​ $ 7,299 ​ $ 5,868 ​ $ 5,097 ​ The table below presents the lease-related assets and liabilities recorded on the Consolidated balance sheets. ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ 2023 ​ 2022 ​ ​ (in thousands) Assets ​ ​ ​ ​ ​ ​ Operating lease right-of-use assets ​ $ 28,789 ​ ​ 32,726 Liabilities ​ ​ ​ ​ ​ ​ Current ​ ​ ​ ​ ​ ​ Current operating lease liabilities ​ ​ 8,344 ​ ​ 8,382 Non-current ​ ​ ​ ​ ​ ​ Non-current operating lease liabilities ​ ​ 28,316 ​ ​ 31,719 Total lease liabilities ​ $ 36,660 ​ ​ 40,101 ​ Other information The weighted-average remaining lease term as of December 31, 2023, is 6.1 years, compared to 7.2 years as of December 31, 2022, and the weighted-average discount rate as of December 31, 2023 is 11.2 % , compared to 11.2 % as of December 31, 2022. The Company uses an incremental borrowing rate applicable to the lease asset. The table below presents supplemental cash flow and non-cash information related to leases. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2023 2022 2021 ​ ​ (in thousands) Cash paid for amounts included in the measurement of lease liabilities ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating cash flows for operating leases ​ $ 7,921 ​ $ 7,532 ​ $ 5,738 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Right-of-use asset obtained in exchange for lease obligation ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating lease ​ $ 561 ​ $ 9,824 ​ $ 1,699 ​ 135 ​ Table of Contents Undiscounted cash flows The table below reconciles the undiscounted cash flows as of December 31, 2023, for each of the first five years and the total of the remaining years to the operating lease liabilities recorded on the Consolidated balance sheet as of December 31, 2023. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Lexington ​ Amsterdam (1) ​ Other ​ Total ​ (in thousands) 2024 $ 5,504 ​ $ 2,569 ​ $ 295 ​ $ 8,368 2025 ​ 5,859 ​ ​ 2,056 ​ ​ 295 ​ ​ 8,210 2026 ​ 6,031 ​ ​ 2,056 ​ ​ 246 ​ ​ 8,333 2027 ​ 6,207 ​ ​ 2,060 ​ ​ — ​ ​ 8,267 2028 ​ 6,388 ​ ​ 1,984 ​ ​ — ​ ​ 8,372 Thereafter ​ 2,956 ​ ​ 5,430 ​ ​ — ​ ​ 8,386 Total lease payments $ 32,945 ​ $ 16,155 ​ $ 836 ​ $ 49,936 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Less: amount of lease payments representing interest payments ​ ( 7,920 ) ​ ​ ( 5,211 ) ​ ​ ( 145 ) ​ ​ ( 13,276 ) Present value of lease payments ​ 25,025 ​ ​ 10,944 ​ ​ 691 ​ ​ 36,660 Less: current operating lease liabilities ​ ( 5,504 ) ​ ​ ( 2,569 ) ​ ​ ( 271 ) ​ ​ ( 8,344 ) Non-current operating lease liabilities $ 19,521 ​ $ 8,375 ​ $ 420 ​ $ 28,316 (1) Payments are due in EUR and have been translated at the foreign exchange rate as of December 31, 2023, of $ 1.10 / €1.00 ​ 11. Intangible assets, net and Goodwill ​ The following table presents the Company’s acquired licenses and acquired IPR&D as of December 31: ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, December 31, ​ ​ 2023 ​ 2022 ​ ​ (in thousands) Acquired licenses ​ $ 2,419 ​ $ 2,346 Less accumulated amortization ​ ​ ( 1,057 ) ​ ​ ( 900 ) Acquired licenses, net ​ $ 1,362 ​ $ 1,446 Acquired IPR&D Intangible Asset ​ 59,119 ​ 57,332 Intangibles, net ​ $ 60,481 ​ $ 58,778 ​ a. Acquired licenses ​ All acquired licenses are owned by uniQure biopharma B.V, a subsidiary of the Company. The remaining weighted average life is 10.5 years as of December 31, 2023 (December 31, 2022 11.5 years). ​ ​ As of December 31, 2023, the estimated future amortization expense for each of the five succeeding years and the period thereafter is as follows: ​ ​ ​ ​ ​ Years Amount ​ ​ (in thousands) 2024 ​ $ 130 2025 ​ 130 2026 ​ 130 2027 ​ 130 2028 ​ 130 Thereafter ​ 712 Total ​ $ 1,362 ​ The amortization expense related to licenses for the year ended December 31, 2023 was $ 0.1 million (December 31, 2022: $ 0.4 million; December 31, 2021: $ 1.2 million). ​ 136 ​ Table of Contents b. Acquired in-process research and development ​ As part of its acquisition of uniQure France SAS as of July 30, 2021, the Company identified certain intangible assets related to an IPR&D Intangible Asset. Refer to Note 3 “uniQure France SAS transaction” . ​ c. Goodwill ​ As part of its acquisition of uniQure France SAS as of July 30, 2021, the Company recorded goodwill. Refer to Note 3 “uniQure France SAS transaction” . ​ ​ 12. Accrued expenses and other current liabilities ​ Accrued expenses and other current liabilities include the following items: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2023 2022 ​ ​ (in thousands) Personnel related accruals and liabilities ​ $ 16,263 ​ $ 17,201 Accruals for goods received from and services provided by vendors-not yet billed ​ ​ 12,834 ​ ​ 11,120 Liability owed to the Purchaser pursuant to the Royalty Financing Agreement ​ ​ 1,437 ​ ​ — Accrued contract fulfillment costs and costs to obtain a contract ​ ​ — ​ ​ 2,250 Total ​ $ 30,534 ​ $ 30,571 ​ ​ ​ ​ ​ ​ ​ ​ 13. Long-term debt ​ On June 14, 2013, the Company entered into a venture debt loan facility with Hercules Capital, Inc. (formerly known as Hercules Technology Growth Capital, Inc.) (“Hercules”), which was amended and restated on June 26, 2014, on May 6, 2016 (“2016 Amended Facility”) and on December 6, 2018 (“2018 Amended Facility”). ​ On January 29, 2021, the Company and Hercules amended the 2018 Amended Facility (“2021 Amended Facility”). Pursuant to the 2021 Amended Facility, Hercules agreed to an additional Facility of $ 100.0 million (“Tranche B”) increasing the aggregate principal amount of the term loan facilities from $ 35.0 million to up to $ 135.0 million. On January 29, 2021, the Company drew down $ 35.0 million of the Tranche B. Advances under Tranche B bore interest at a rate equal to the greater of (i) 8.25 % or (ii) 8.25 % plus the prime rate, less 3.25 % per annum. The principal balance of $ 70.0 million and all accrued but unpaid interest on advances under Tranche B was due on June 1, 2023, which date could have been extended by the Company by up to two twelve-month periods. In addition to Tranche B, the 2021 Amended Facility had also extended the interest only payment period of the previously funded $ 35.0 million term loan (“Tranche A”) from January 1, 2022 to June l, 2023. ​ On December 15, 2021, the Company and Hercules amended and restated the 2021 Amended Facility (“2021 Restated Facility”). Pursuant to the 2021 Restated Facility, Tranche A and Tranche B of the 2021 Amended Facility with a total outstanding balance of $ 70.0 million were consolidated into one tranche with a total commitment of $ 100.0 million. The Company drew down an additional $ 30.0 million, resulting in total principal outstanding as of December 31, 2021 of $ 100.0 million. The 2021 Restated Facility extended the loan’s maturity date from June 1, 2023 until December 1, 2025. The interest-only period was extended from January 1, 2023 to December 1, 2024, or December 1, 2025 if, prior to June 30, 2024, either (a) the BLA for AMT-061 had been approved by the U.S. Food and Drug Administration (“FDA”) or (b) AMT-130 had advanced into a pivotal trial. On November 22, 2022, the FDA approved the BLA for AMT-061 resulting in the extension of the interest-only period to December 1, 2025. ​ On May 12, 2023 the Company and Hercules amended the 2021 Restated Facility (the “2023 Amended Facility”). The total principal outstanding under the 2023 Amended Facility remained $ 100.0 million. The 2023 Amended Facility extended the maturity date and interest only period from December 1, 2025 to January 5, 2027 (the “Maturity Date”). 137 ​ Table of Contents The Company is required to repay the entire principal balance on the Maturity Date. The interest rate is adjustable and is the greater of (i) 7.95 % and (ii) 7.95 % plus the prime rate less 3.25 % per annum. The Company paid a $ 2.5 million back-end fee in June 2023. Under the 2023 Amended Facility, the Company owes a back-end fee of $ 4.9 million on December 1, 2025 and a back-end fee of $ 1.3 million on the Maturity Date. ​ The amortized cost (including interest due presented as part of accrued expenses and other current liabilities) of the 2023 Amended Facility was $ 102.9 million as of December 31, 2023, compared to an amortized cost of $ 103.8 million as of December 31, 2022, and is recorded net of discount and debt issuance costs. The foreign currency gain on the loan was $ 3.0 million in 2023 (2022: loss of $ 5.8 million; 2021: loss of $ 5.3 million). The fair value of the loan approximates its carrying amount. Inputs to the fair value of the loan are considered Level 3 inputs. ​ Interest expense recorded during the years ended December 31 was as follows: ​ ​ ​ ​ ​ Years Amount ​ ​ (in millions) 2023 ​ $ 14.6 2022 ​ 11.5 2021 ​ ​ 7.2 ​ Under the 2023 Amended Facility the Company must remain current in its periodic reporting requirements and is required to keep a minimum cash balance deposited in bank accounts in the United States, equivalent to the lesser of (i) 65 % of the outstanding balance of principal due or (ii) 100 % of worldwide cash and cash equivalents. This restriction on cash and cash equivalents only relates to the location of the cash and cash equivalents, and such cash and cash equivalents can be used at the discretion of the Company. Beginning on April 1, 2024, the Company is required to keep a minimum of unrestricted cash of at least 30 % of the loan amount outstanding. In combination with other covenants, the 2023 Amended Facility restricts the Company’s ability to, among other things, incur future indebtedness and obtain additional debt financing, to make investments in securities or in other companies, to transfer assets, to perform certain corporate changes, to make loans to employees, officers, and directors, and to make dividend payments and other distributions to its shareholders. The Company secured the facilities by directly or indirectly pledging its total assets of $ 831.7 million, less $ 9.3 million of cash and cash equivalents and other current assets held by the Company and $ 90.4 million of other current assets and investment held by uniQure France SAS as well as receivables sold to the Purchaser. ​ Under the 2023 Amended Facility, the occurrence of a material adverse effect, as defined therein, would entitle Hercules to declare all principal, interest and other amounts owed by the Company immediately due and payable. As of December 31, 2023, the Company was in material compliance with all covenants and provisions. ​ The aggregate maturities of the loans, including $ 47.6 million of coupon interest payments and financing fees, for each of the 37 months after December 31, 2023, are as follows: ​ ​ ​ ​ ​ Years Amount ​ ​ (in thousands) 2024 ​ $ 13,420 2025 ​ ​ 18,233 2026 ​ ​ 13,383 2027 ​ ​ 102,533 Total ​ $ 147,569 ​ ​ 138 ​ Table of Contents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 14. Royalty Financing Agreement ​ On May 12, 2023, the Company entered into the Royalty Financing Agreement with the Purchaser. Under the terms of the Royalty Financing Agreement the Company received an upfront payment of $ 375.0 million in exchange for its rights to the lowest royalty tier on CSL Behring’s worldwide net sales of HEMGENIX® for certain current and future royalties due to the Company. The Company is also eligible to receive an additional $ 25.0 million milestone payment under the Royalty Financing Agreement if 2024 net sales of HEMGENIX® exceed a pre-specified threshold, as set forth in the Royalty Financing Agreement. The Purchaser will receive 1.85 times the upfront payment (or $ 693.8 million) and 1.85 times the $ 25.0 million milestone payment (if paid) until June 30, 2032 (“First Hard Cap Date”) if such thresholds are met or, if such cap is not met by June 30, 2032, up to 2.25 times of the upfront and milestone payment (if paid) through December 31, 2038. If 2024 net sales do not exceed a pre-specified threshold, the Company will be obligated to pay $ 25.0 million to the Purchaser but only to the extent that the Company achieves a future sales milestone under the CSL Behring Agreement. If such milestone payment is not due from CSL Behring, the Company is not obligated to pay any amounts to the Purchaser. ​ The Company has retained the rights to all other royalties, as well as commercial milestones totaling up to $ 1.3 billion, under the terms of the CSL Behring Agreement. ​ Net proceeds from the Royalty Financing Agreement, after deducting professional and financial advisory fees related to the transaction of $ 4.9 million, were $ 370.1 million. The Company initially recorded these net proceeds as “Liability from royalty financing agreement” at their fair market value on its balance sheet as of closing of the transaction on June 5, 2023. Following the initial recognition, the Company records the debt at amortized cost. ​ The Company expects to satisfy its commitment to the Purchaser prior to the First Hard Cap Date. The Company will record the difference of $ 323.7 million between the total expected payments of $ 693.8 million to the Purchaser and the $ 370.1 million net proceeds as interest expense using the effective interest rate method. The Company determined the effective interest rate based on the projected cash flows up to the First Hard Cap Date. Based on the Company’s projections the effective interest rate is expected to be within a range of 12.0 % to 13.5 % per annum. The Company would have recorded between $ 26.5 million and $ 29.9 million of interest expense during the year ended December 31, 2023 ( nil for the year ended December 31, 2022 and 2021) if it had used effective interest rates of 12.0 % or 13.5 %, instead of the $ 26.9 million recorded in the during the year ended December 31, 2023 ( nil for the year ended December 31, 2022 and 2021). The Company will prospectively update the effective interest rate at each reporting date based on updated projections. ​ The liability was initially recognized at fair value and inputs were considered Level 3 inputs. ​ The following table presents the movement in the liability related to the Royalty Financing Agreement between the closing of the transaction on June 5, 2023 and December 31, 2023: ​ ​ ​ ​ ​ ​ ​ ​ Amount of liability ​ ​ ​ (in thousands) Gross proceeds from royalty financing agreement on June 5, 2023 ​ $ 375,000 Debt issuance costs paid ​ ​ ( 4,938 ) Royalty payments to Purchaser ​ ​ ( 1,317 ) Liability owed to the Purchaser (presented as "Accrued expense and other current liabilities") ​ ​ ( 1,437 ) Interest expense for the period June 5, 2023 to December 31, 2023 ​ ​ 26,933 Liability related to the royalty financing agreement ​ $ 394,241 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 139 ​ Table of Contents ​ ​ 15. Retirement benefits ​ Defined benefit pension plan ​ The Company operates a defined benefit pension plan for its Swiss employees (the “Swiss Plan”) in accordance with local regulations and practices. The normal retirement age under the Swiss Plan is 65 for men and women. All benefits are immediately vested. Under the Swiss Plan, a percentage of pensionable salary is contributed as a retirement credit with additional contributions being made for death and disability benefits. Under Swiss pension law, participants who are covered by the pension plan of another employer are required to transfer the termination benefit of that pension plan into the plan of the Company. When employment at the Company ends before reaching retirement, the termination benefit is transferred out of the defined benefit pension plan. At time of retirement the accumulated retirement credit can be converted into a life-long annuity or be paid-out as a lump-sum. Participants are also permitted to withdraw a part of the accumulated termination benefit in special circumstances before reaching retirement age for example for payments related to obtain home ownership. ​ The Company recognized its net projected benefit obligation as of December 31, 2023 at a carrying amount of $ 2.5 million, presented within other non-current liabilities in the consolidated balance sheets. ​ The funded status of the Swiss Plan as of December 31, 2023 is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ 2023 ​ ​ ​ (in thousands) Fair value of plan assets ​ ​ $ 8,946 Present value of projected benefit obligation ​ ​ ​ ( 11,499 ) Funded status: (net liability) ​ ​ $ ( 2,553 ) ​ ​ ​ ​ ​ Accumulated benefit obligation as of December 31, 2023 ​ ​ $ 10,739 ​ Actuarial losses of $ 2.1 million, net of $ 0.4 million deferred tax income, were recorded in other comprehensive income, net, during the year ended December 31, 2023. ​ The assumptions related to the Swiss Plan are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, Actuarial assumptions (% p.a.) 2023 Discount rate ​ ​ ​ 1.50 % Expected return on plan assets ​ ​ ​ 2.60 % Expected inflation rate ​ ​ ​ 1.60 % Interest credit rate ​ ​ ​ 1.25 % Long-term expected rate of salary increases ​ ​ ​ 1.60 % Pension increase ​ ​ ​ 0.00 % ​ Future benefits expected to be paid are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ 2023 Year 1 ​ ​ $ 533 Year 2 ​ ​ ​ 610 Year 3 ​ ​ ​ 528 Year 4 ​ ​ ​ 529 Year 5 ​ ​ ​ 540 Next 5 years ​ ​ ​ 4,992 ​ ​ ​ ​ ​ Other disclosure items: ​ ​ ​ ​ Next year's expected employer contribution ​ ​ $ 552 ​ ​ ​ ​ ​ ​ 140 ​ Table of Contents The Company's investment strategy for its pension plan is to optimize the long-term investment return on plan assets in relation to the liability structure to maintain an acceptable level of risk while minimizing the cost of providing pension benefits and maintaining adequate funding levels in accordance with the applicable rules in each jurisdiction. The Company does not manage any assets internally. The plan assets relate to assets being held by the Swiss pension foundations in which the Company's pension plan is set-up. ​ The allocation of plan assets is presented below: ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ 2023 Bonds ​ ​ 61 % Equities ​ ​ 25 % Real estate ​ ​ 10 % Others ​ ​ 4 % ​ The fair value of the plan assets is determined based on Level 2 inputs. ​ ​ 16. Shareholders’ equity ​ As of December 31, 2023, the Company’s authorized share capital is € 4.0 million (or $ 4.4 million when translated at an exchange rate as of December 31, 2023, of $ 1.10 / €1.00), divided into 80,000,000 ordinary shares, each with a nominal value of € 0.05 . The Company’s shareholders, at the 2021 Annual General Meeting of Stockholders held on June 16, 2021, approved an increase in the number of authorized ordinary shares by 20,000,000 to 80,000,000 . ​ All ordinary shares issued by the Company were fully paid. Besides the minimum amount of share capital to be held under Dutch law, there are no distribution restrictions applicable to the equity of the Company. ​ As of December 31, 2023, and 2022 and 2021 the Company’s other comprehensive result was restricted for payment of dividends for an accumulated other comprehensive loss of $ 53.6 million in 2023, an accumulated other comprehensive loss of $ 58.3 million in 2022, and an accumulated other comprehensive loss of $ 28.9 million in 2021. ​ On March 1, 2021, the Company entered into a Sales Agreement with SVB Leerink LLC (“SVB Leerink”) with respect to an at-the-market (“ATM”) offering program, under which the Company may, from time to time in its sole discretion, offer and sell through SVB Leerink, acting as agent, its ordinary shares, up to an aggregate offering price of $ 200.0 million. The Company will pay SVB Leerink a commission equal to 3 % of the gross proceeds of the sales price of all ordinary shares sold through it as sales agent under the Sales Agreement. In March and April 2021, the Company issued an aggregate of 921,730 ordinary shares at a weighted average price of $ 33.52 per ordinary share, with net proceeds of $ 29.6 million, after deducting underwriting discounts and net of offering expenses. The Company defers direct, incremental costs associated to this offering, except for the commission costs to SVB Leerink, which are a reduction to additional paid-in capital and will deduct these costs from additional paid-in capital in the consolidated balance sheets proportionately to the amount of proceeds raised. During the year ended December 31, 2021, $ 1.3 million of direct, incremental costs were deducted from additional paid-in capital ( nil for the years ended December 31, 2022 and 2023). ​ Following the Closing of the CSL Behring transaction, the Company consumed its tax net operating loss carryforwards from the years 2011 to 2018. The Company allocated the tax benefit from the release of the valuation allowance related to net operating loss carryforwards generated by share issuance costs incurred in 2014, 2015, 2017 and 2018 to additional paid-in capital. This resulted is an increase of additional paid-in capital of $ 3.0 million in the year ended December 31, 2021. ​ The Company recorded a $ 0.8 million increase of additional paid-in capital in the year ended December 31, 2022 resulting from the release of valuation allowance for the tax benefit of share issuance costs incurred in 2018, 2019 and 2021 within the Netherlands. ​ ​ ​ 141 ​ Table of Contents 17. Share-based compensation ​ Share-based compensation expense recognized by classification included in the consolidated statements of operations and comprehensive (loss) / income was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ 2023 ​ 2022 ​ 2021 ​ ​ (in thousands) Cost of manufacturing services revenue ​ $ 826 ​ $ 323 ​ $ — Research and development ​ ​ 16,881 ​ ​ 18,402 ​ ​ 12,834 Selling, general and administrative ​ ​ 17,386 ​ ​ 15,479 ​ ​ 12,801 Total ​ $ 35,093 ​ $ 34,204 ​ $ 25,635 ​ Share-based compensation expense recognized by award type was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ 2023 ​ 2022 ​ 2021 ​ ​ (in thousands) Award type/ESPP ​ ​ ​ ​ ​ ​ ​ ​ ​ Share options ​ $ 13,302 ​ $ 13,425 ​ $ 12,477 Restricted share units ​ ​ 18,524 ​ ​ 15,486 ​ ​ 11,347 Performance share units ​ ​ 3,234 ​ ​ 5,267 ​ ​ 1,783 Employee share purchase plan ​ ​ 33 ​ ​ 26 ​ ​ 28 Total ​ $ 35,093 ​ $ 34,204 ​ $ 25,635 ​ As of December 31, 2023, the unrecognized compensation cost related to unvested awards under the various share-based compensation plans were: ​ ​ ​ ​ ​ ​ ​ ​ Unrecognized Weighted average ​ share-based remaining ​ ​ compensation ​ period for ​ ​ expense ​ recognition ​ ​ (in thousands) ​ (in years) Award type ​ ​ ​ ​ ​ Share options ​ $ 21,708 ​ 2.47 Restricted share units ​ ​ 27,015 ​ 1.89 Performance share units ​ ​ 738 ​ 0.95 Total ​ $ 49,461 ​ 2.13 ​ The Company satisfies the exercise of share options and vesting of Restricted Share Units (“RSUs”) and Performance Share Units (“PSUs”) through newly issued ordinary shares. ​ The Company’s share-based compensation plans include the 2014 Amended and Restated Share Option Plan (the “2014 Plan”) and inducement grants under Rule 5653(c)(4) of The Nasdaq Global Select Market with terms similar to the 2014 Plan (together the “2014 Plans”). The Company previously had a 2012 Equity Incentive Plan (the “2012 Plan”). As of December 31, 2023, no fully vested share options are outstanding (December 31, 2022: nil ) under the 2012 Plan. ​ At the general meeting of shareholders on January 9, 2014, the Company’s shareholders approved the adoption of the 2014 Plan. At the annual general meetings of shareholders in June 2015, 2016, 2018 and 2021, uniQure shareholders approved amendments of the 2014 Plan, increasing the shares authorized for issuance by 1,070,000 shares in 2015, 3,000,000 in 2016, 3,000,000 shares in 2018, 4,000,000 shares in 2021. At an extraordinary general meeting of shareholders in November 2023, an additional 1,750,000 shares were authorized for issuance, increasing the total to 14,351,471 shares. ​ ​ 142 ​ Table of Contents Share options Share options are priced on the date of grant and, except for certain grants made to non-executive directors, vest over a period of four years . The first 25 % vests after one year from the initial grant date and the remainder vests in equal quarterly installments over years two, three and four. Certain grants to non-executive directors vest in full after one year . Any options that vest must be exercised by the tenth anniversary of the initial grant date. 2014 Plans The following tables summarize option activity under the Company’s 2014 Plans for the year ended December 31, 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Options ​ ​ Number of ​ Weighted average ​ Weighted average ​ Aggregate intrinsic ​ ordinary shares exercise price remaining contractual life value ​ ​ ​ ​ ​ ​ ​ in years ​ ​ (in thousands) Outstanding at December 31, 2022 ​ 4,237,917 ​ $ 26.13 ​ 7.14 ​ $ 17,848 Granted ​ 1,650,030 ​ $ 18.16 ​ ​ ​ ​ ​ Forfeited ​ ( 543,481 ) ​ $ 22.04 ​ ​ ​ ​ ​ Expired ​ ( 356,366 ) ​ $ 36.26 ​ ​ ​ ​ ​ Exercised ​ ( 14,070 ) ​ $ 9.24 ​ ​ ​ ​ ​ Outstanding at December 31, 2023 ​ 4,974,030 ​ $ 23.25 ​ 6.71 ​ ​ 182 Thereof, fully vested, and exercisable on December 31, 2023 ​ 2,738,595 ​ $ 26.08 ​ 5.15 ​ ​ 182 Thereof, outstanding and expected to vest after December 31, 2023 ​ 2,235,435 ​ $ 19.78 ​ 8.77 ​ ​ — Outstanding and expected to vest after December 31, 2022 ​ 2,098,557 ​ $ 23.38 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of options issued during the period (in $ millions) ​ ​ ​ $ 17.4 ​ ​ ​ ​ ​ Granted to directors and officers during the period (options, grant date fair value $ in millions) ​ 786,580 ​ $ 9.0 ​ ​ ​ ​ ​ Proceeds from option sales during the period (in $ millions) ​ ​ ​ $ 0.1 ​ ​ ​ ​ ​ ​ The following table summarizes information about the weighted average grant-date fair value of options during the years ended December 31: ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted average ​ ​ Options ​ grant ‑ date fair value Granted, 2023 1,650,030 ​ $ 10.57 Granted, 2022 1,426,966 ​ ​ 9.04 Granted, 2021 1,174,893 ​ ​ 20.95 Vested, 2023 ​ 873,658 ​ ​ 13.50 Forfeited, 2023 ​ ( 543,481 ) ​ ​ 12.78 ​ The following table summarizes information about the weighted average grant-date fair value of options at December 31: ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted average ​ ​ Options ​ grant ‑ date fair value Outstanding and expected to vest, 2023 2,235,435 ​ $ 11.50 Outstanding and expected to vest, 2022 2,098,557 ​ ​ 13.46 ​ ​ 143 ​ Table of Contents The fair value of each option issued is estimated at the respective grant date using the Hull & White option pricing model with the following weighted-average assumptions: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, Assumptions 2023 2022 ​ 2021 Expected volatility ​ 70 % ​ 70 % ​ 75 % Expected terms ​ 10 years ​ 10 years ​ 10 years Risk free interest rate ​ 3.7 % - 4.8 % ​ 2.1 % - 4.2 % ​ 1.2 - 1.9 % Expected dividend yield ​ 0 % ​ 0 % ​ 0 % ​ The Hull & White option model captures early exercises by assuming that the likelihood of exercises will increase when the share price reaches defined multiples of the strike price. This analysis is performed over the full contractual term. ​ The following table summarizes information about options exercised during the years ended December 31: ​ ​ ​ ​ ​ ​ ​ ​ Exercised ​ ​ ​ ​ during the year ​ Intrinsic value ​ ​ ​ ​ (in thousands) 2023 14,070 ​ $ 154 2022 138,356 ​ 1,848 2021 241,496 ​ 5,046 ​ Restricted Share Units ​ The following table summarizes the RSU activity for the year ended December 31, 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ RSUs ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2022 ​ 1,818,774 ​ $ 20.46 Granted ​ 1,770,025 ​ $ 17.88 Vested ​ ( 738,447 ) ​ $ 22.65 Forfeited ​ ( 585,983 ) ​ $ 19.12 Non-vested at December 31, 2023 ​ 2,264,369 ​ $ 18.07 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of RSUs granted during the period (in $ millions) ​ ​ ​ $ 31.6 Granted to directors and officers during the period (shares, $ in millions) ​ 419,200 ​ $ 8.3 ​ The following table summarizes information about the weighted average grant-date fair value of RSUs granted during the years ended December 31: ​ ​ ​ ​ ​ ​ ​ ​ Granted Weighted average ​ ​ during the year ​ grant ‑ date fair value 2023 1,770,025 ​ $ 17.88 2022 1,604,533 ​ ​ 16.10 2021 574,921 ​ ​ 36.14 ​ The following table summarizes information about the total fair value of RSUs that vested during the years ended December 31: ​ ​ ​ ​ ​ Total fair value ​ (in thousands) 2023 $ 13,729 2022 5,104 2021 8,063 ​ 144 ​ Table of Contents RSUs generally vest over one to three years . RSUs granted to non-executive directors will vest one year from the date of grant. ​ Performance Share Units ​ The following table summarizes the PSU activity for the year ended December 31, 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ PSUs ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2022 ​ 400,690 ​ $ 28.82 Vested ​ ( 94,510 ) ​ $ 30.65 Forfeited ​ ( 83,630 ) ​ $ 28.22 Non-vested at December 31, 2023 ​ 222,550 ​ $ 28.09 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of PSUs granted during the period (in $ millions) ​ ​ ​ $ - ​ The Company granted shares to certain employees in September and December 2021 and various dates during the year ended December 31, 2022 that will be earned upon achievement of defined milestones. Earned shares will vest upon the later of a minimum service period of three years , or the achievement of defined milestones, subject to the grantee’s continued employment. In addition, portions of the December 2021 granted to executives and other members of senior management are subject to achieving a minimum total shareholder return relative to the Nasdaq biotechnology index. The Company recognizes the compensation cost related to these grants to the extent it considers achievement of the milestones to be probable. As of December 31, 2023, two milestones had been achieved and vested in either 2022 or 2023. Additionally, another two milestones are considered probable as of December 31, 2023. ​ In January 2018 and January and February 2019, the Company awarded PSUs to its executives and other members of senior management. These PSUs were earned in January 2019 and January 2020, based on the Board of Directors’ (the “Board”) assessment of the level of achievement of agreed upon performance targets through December 31, 2018, and December 31, 2019, respectively. The PSUs awarded for the year ended December 31, 2018 vested in February 2021 and the PSUs awarded for the year ended December 31, 2019 vested in January 2022. ​ The following table summarizes information about the weighted average grant-date fair value of the PSUs determined as of the date of the grant for the 2021 and 2022 PSUs: ​ ​ ​ ​ ​ ​ ​ ​ Granted Weighted average ​ ​ during the year ​ grant ‑ date fair value 2023 — ​ $ — 2022 34,700 ​ $ 15.11 2021 555,600 ​ $ 30.19 ​ The following table summarizes information about the total fair value of PSUs that vested during the years ended December 31: ​ ​ ​ ​ ​ Total fair value ​ (in thousands) 2023 $ 1,474 2022 4,450 2021 5,074 ​ 145 ​ Table of Contents Employee Share Purchase Plan (“ESPP”) ​ In June 2018, the Company’s shareholders adopted and approved an ESPP allowing the Company to issue up to 150,000 ordinary shares. The ESPP is intended to qualify under Section 423 of the Internal Revenue Code of 1986. Under the ESPP, employees are eligible to purchase ordinary shares through payroll deductions, subject to any plan limitations. The purchase price of the shares on each purchase date is equal to 85 % of the lower of the closing market price on the offering date or the closing market price on the purchase date of each three-month offering period. During the year ended December 31, 2023, 19,198 ordinary shares have been issued (December 31, 2022: 11,242 and December 31, 2021: 4,724 ). As of December 31, 2023, a total of 96,862 ordinary shares remain available for issuance under the ESPP plan. ​ ​ 18. Expenses by nature ​ Operating expenses excluding expenses presented in other expenses included the following expenses by nature: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2023 2022 2021 ​ ​ (in thousands) Employee-related expenses ​ $ 135,728 ​ $ 119,903 ​ $ 96,161 Laboratory and development expenses ​ 63,065 ​ 65,964 ​ 36,014 Office and housing expenses ​ 22,960 ​ 17,612 ​ 14,638 Legal and advisory expenses ​ ​ 21,975 ​ 15,782 ​ 24,767 Fair value loss - uniQure France SAS contingent consideration ​ ​ 15,895 ​ 7,081 ​ 6,683 Other operating expenses ​ 11,236 ​ 8,510 ​ 10,528 Depreciation and amortization expenses ​ 10,046 ​ 8,250 ​ 7,299 Patent and license expenses ​ ​ 7,112 ​ ​ 9,548 ​ ​ 3,748 Impairment related to the Reorganization ​ ​ 1,438 ​ ​ — ​ ​ — Total ​ $ 289,455 ​ $ 252,650 ​ $ 199,838 ​ Details of employee-related expenses for the years ended December 31 are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2023 2022 2021 ​ ​ (in thousands) Wages and salaries ​ $ 71,852 ​ $ 63,704 ​ $ 53,078 Share-based compensation expenses ​ 34,267 ​ 33,881 ​ 25,635 Contractor expenses ​ 6,141 ​ 3,959 ​ 3,170 Social security costs ​ 5,900 ​ 5,179 ​ 4,496 Health insurance ​ 4,216 ​ 4,148 ​ 3,161 Costs related to pension plans ​ 3,611 ​ 2,667 ​ 2,051 Severance costs related to the Reorganization (refer to Note 4 " Reorganization ") ​ ​ 2,549 ​ ​ — ​ ​ — Other employee expenses ​ ​ 7,192 ​ ​ 6,365 ​ ​ 4,570 Total ​ $ 135,728 ​ $ 119,903 ​ $ 96,161 ​ ​ ​ ​ 19. Other income ​ Other income during the year ended December 31, 2023 was $ 6.1 million compared to $ 7.2 million and $ 12.3 million during the same periods in 2022 and 2021, respectively. ​ Other income in 2023, 2022 and 2021 includes income from payments received from European authorities to subsidize the Company’s research and development efforts in the Netherlands. The amount recognized in the year ended December 31, 2023 was $ 5.0 million compared to $ 5.6 million in 2022 and $ 5.3 million in 2021. ​ 146 ​ Table of Contents In addition, other income included $ 2.6 million of employee retention credits received under the U.S. Coronavirus Aid, Relief, and Economic Security Act, during the year ended December 31, 2021. No such income was received in the years ended December 31, 2023 or December 31, 2022. ​ An additional $ 3.0 million of other income was recorded in the year ended December 31, 2021, related to the receipt by the Company of 69,899 shares of VectorY B.V. in conjunction with a settlement agreement that the Company and VectorY B.V. entered into in April 2021. In the year ended December 31, 2023 and 2022, the Company recognized nil and $ 0.3 million, respectively, of other income related to the equity stake received in VectorY. ​ In 2023, 2022 and 2021 the Company’s other income also consisted of income from the subleasing of a portion of the Amsterdam facility while other expense consists of expenses incurred in relation to the subleasing income. ​ ​ ​ 20. Income taxes ​ a. Income tax (benefit) / expense ​ Due to the uncertainty surrounding the realization of favorable tax attributes in future tax returns, the Company has recorded a valuation allowance against the Company’s net deferred tax assets in the Netherlands and a partial valuation allowance against the Company’s net deferred tax assets in France. ​ In connection with the acquisition of uniQure France SAS, the Company recognized a deferred tax liability related to acquired identifiable intangible assets and a deferred tax asset for net operating tax loss carryforwards for a net of EUR 11.9 million ($ 14.2 million) as of the Acquisition Date. ​ There are no significant unrecognized tax benefits as of December 31, 2023 and 2022. ​ For the years ended December 31, 2023, 2022 and 2021, (loss) / income before income tax benefit / (expense) consists of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2023 2022 2021 ​ ​ (in thousands) Dutch operations ​ $ ( 282,530 ) ​ $ ( 96,872 ) ​ $ 348,400 U.S. operations ​ ( 6,903 ) ​ ( 14,934 ) ​ ( 12,737 ) Other ​ ​ ( 17,124 ) ​ ​ ( 16,453 ) ​ ​ ( 2,857 ) Total ​ $ ( 306,557 ) ​ $ ( 128,259 ) ​ $ 332,806 ​ The income tax (expense) / benefit for the years ended December 31, 2023, 2022 and 2021, consists of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2023 2022 2021 ​ ​ (in thousands) Current tax expense ​ ​ ​ ​ ​ ​ ​ ​ ​ Other ​ $ ( 110 ) ​ $ ( 24 ) ​ $ ( 7 ) Total current income tax expense ​ $ ( 110 ) ​ $ ( 24 ) ​ $ ( 7 ) Deferred tax (expense) / benefit ​ ​ ​ ​ ​ ​ Dutch operations ​ $ — ​ $ ( 808 ) ​ $ ( 3,047 ) U.S. operations ​ ( 2,708 ) ​ ( 1,075 ) ​ ( 771 ) Other ​ ​ 897 ​ ​ 3,377 ​ ​ 608 Total deferred tax (expense) / benefit ​ $ ( 1,811 ) ​ $ 1,494 ​ $ ( 3,210 ) Total income tax (expense) / benefit ​ $ ( 1,921 ) ​ $ 1,470 ​ $ ( 3,217 ) ​ 147 ​ Table of Contents b. Tax benefit recognized in other comprehensive income ​ The reconciliation of the amount of income tax benefit recognized in other comprehensive income for the year ended December 31, 2023 is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, 2023 ​ Before tax Tax benefit Net of tax ​ ​ (in thousands) Unrecognized gain related to defined benefit pension plan liability ​ $ ( 2,553 ) ​ $ 417 ​ $ ( 2,136 ) Total ​ $ ( 2,553 ) ​ $ 417 ​ $ ( 2,136 ) ​ No income tax benefit or expense has been recognized in Other Comprehensive Income for the years ended December 31, 2022 and 2021. ​ c. Tax rate reconciliation ​ The reconciliation of the amount of income tax (expense) / benefit that would result from applying the Dutch statutory income tax rate to the Company’s reported amount of (loss) / income before income tax (expense) / benefit for the years ended December 31, 2023, 2022 and 2021, is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ 2023 ​ 2022 ​ 2021 ​ ​ (in thousands) (Loss) / income before income tax (expense) / benefit for the period ​ $ ( 306,557 ) ​ $ ( 128,259 ) ​ $ 332,806 Expected income tax benefit / (expense) at the tax rate enacted in the Netherlands (2023: 25.8 %, 2022: 25.8 %, 2021: 25.0 %) ​ 79,092 ​ 33,091 ​ ( 83,201 ) Difference in tax rates between the Netherlands and the U.S. as well as other foreign countries ​ ( 124 ) ​ 99 ​ 309 Other net change in valuation allowance ​ ( 67,004 ) ​ ( 20,591 ) ​ 88,857 Non-deductible expenses ​ ( 13,885 ) ​ ( 11,129 ) ​ ( 9,182 ) Income tax (expense) / benefit ​ $ ( 1,921 ) ​ $ 1,470 ​ $ ( 3,217 ) ​ Non-deductible expenses predominantly relate to share-based compensation expenses. These expenses affected the effective tax rate by an amount of $ 9.0 million in 2023 (2022: $ 8.5 million; 2021: $ 6.7 million). The fair value loss on contingent consideration affected the effective tax rate by an amount of $ 4.1 million in 2023 ($ 1.9 million and $ 2.0 million in 2022 and 2021, respectively). ​ 148 ​ Table of Contents d. Significant components of deferred taxes ​ The tax effects of temporary differences and carryforwards that give rise to significant portions of deferred tax assets and deferred tax liabilities as of December 31, 2023 and 2022 are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ 2023 ​ 2022 ​ ​ (in thousands) Deferred tax assets: ​ ​ Net operating loss carryforwards ​ $ 145,826 ​ $ 84,633 Operating lease liabilities ​ ​ 9,790 ​ ​ 10,612 Intangible assets ​ 6,417 ​ 3,826 Liability from Royalty Financing Agreement ​ ​ 6,155 ​ ​ — Interest carryforwards ​ ​ 3,711 ​ ​ 3,697 Accrued expenses and other current liabilities ​ ​ 1,435 ​ ​ 1,862 Inventory ​ ​ 497 ​ ​ — Defined benefit pension plan liability ​ ​ 406 ​ ​ — Property, plant and equipment ​ — ​ 510 Research and development tax credit carryforwards ​ ​ — ​ ​ 144 Total deferred tax assets ​ $ 174,237 ​ $ 105,284 Less valuation allowance ​ ( 145,191 ) ​ ( 74,547 ) Deferred tax assets, net of valuation allowance ​ $ 29,046 ​ $ 30,737 Acquired IPR&D intangible asset ​ ​ ( 15,242 ) ​ ​ ( 15,033 ) Operating lease right-of-use assets ​ ​ ( 8,159 ) ​ ​ ( 9,323 ) Property, plant and equipment ​ ​ ( 719 ) ​ ​ — Other current assets and receivables ​ ​ ( 193 ) ​ ​ ( 110 ) Deferred tax liability ​ $ ( 24,313 ) ​ $ ( 24,466 ) Net deferred tax asset ​ $ 4,733 ​ $ 6,271 ​ Changes in the valuation allowance were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2023 2022 2021 ​ ​ (in thousands) January 1, ​ $ 74,547 ​ $ 60,289 ​ $ 150,113 Changes recorded in the statement of operations ​ ​ 67,004 ​ ​ 20,593 ​ ​ ( 88,858 ) Changes recorded in equity ​ ​ — ​ ​ ( 972 ) ​ ​ — Increase related to 2021 Dutch tax reforms ​ — ​ — ​ 1,897 Valuation allowance assumed in uniQure France SAS acquisition ​ ​ — ​ ​ — ​ ​ 545 Other changes including currency translation adjustments ​ 3,640 ​ ( 5,363 ) ​ ​ ( 3,408 ) December 31, ​ $ 145,191 ​ $ 74,547 ​ $ 60,289 ​ The valuation allowance as of December 31, of $ 145.2 million as of December 31,2023 is primarily related to $ 142.4 million deferred tax assets in the Netherlands resulting from net operating loss carryforwards of $ 127.1 million, intangibles assets of $ 5.5 million, liability from Royalty Financing Agreement of $ 6.2 million and interest carryforwards of $ 3.7 million. ​ Netherlands ​ As of December 31, 2023, the total amount of net operating losses carried forward under the Dutch tax regime was $ 492.7 million (December 31, 2022: $ 264.0 million, 2021: $ 228.5 million). The Company has historically recorded a full valuation allowance. The Company evaluates all positive and negative evidence in assessing the need for a full valuation allowance. Management considers reversing taxable temporary differences, projected future taxable income and tax-planning strategies in making this assessment. The Company concluded that as of December 31, 2023, December 31, 2022 and December 31, 2021 it is more likely than not that the remaining deferred tax assets will not be realized. ​ 149 ​ Table of Contents As of December 31, 2023, the tax treatment of the Royalty Agreement has not yet been agreed with the Dutch tax authorities. A different tax treatment could result in a different categorization of temporary differences and an offsetting deferred tax asset. ​ The Company recorded $ 462.4 million of license revenue in May 2021 after the Closing of the CSL Behring transaction. The Company recorded such revenue in its Dutch tax return related to the 12-month period ended December 31, 2020, which it filed on February 10, 2022. As such, the Company filed a return showing a taxable profit in the Netherlands in 2020, which resulted in the consumption of substantially all of its Dutch net operating losses for the years 2011 to 2018. The Company’s remaining Dutch net operating tax losses carried forward relate to 2019, 2022 and 2023. The Company allocated the tax benefit from the release of the valuation allowance related to net operating loss carryforwards generated by share issuance cost incurred in 2014, 2015, 2017 and 2018 to additional paid-in capital. This resulted in an increase of additional paid-in capital as well as deferred tax expenses of $ 3.0 million during the year ended December 31, 2021. ​ The Company recorded $ 0.8 million increase of additional paid-in capital in the year ended December 31, 2022 resulting from the release of valuation allowance for the tax benefit of share issuance costs incurred in 2018, 2019 and 2021. ​ A portion of the valuation allowance for deferred tax assets recorded as of December 31, 2023 continues to relate to follow-on offering costs incurred in 2019. Any subsequently recognized tax benefits will be credited directly to contributed capital. As of December 31, 2023, that amount was $ 3.4 million ($ 3.3 million as of December 31, 2022). ​ The Dutch corporate tax rate for fiscal year 2021 was 25.0 %. In December 2021, changes were enacted that raised the corporate income tax rate from 25.0 % to 25.8 % from 2022 onwards. ​ In June 2021 legislation was enacted allowing for an indefinite carryforward from fiscal year 2022 onwards of existing and future net operating loss carryforwards subject to a limit of offsetting taxable profit in excess of EUR 1.0 million to 50% of the taxable profit. ​ The fiscal periods from 2022 onwards are still open for inspection by the Dutch tax authorities. ​ United States of America ​ The federal corporate tax rate in the U.S. is 21.0 %. In addition, the Company is subject to state income taxes resulting in a combined tax rate of 27.3 % for its U.S. operation. As of December 31, 2023, an estimated $ 31.1 million of net operating losses remain to be carried forward. These net operating losses carried forward will expire in 2036 and 2037 except for $ 0.7 million which can be carried forward indefinitely with a deduction limited to 80% of taxable income in a given year. ​ The Company’s U.S. operations generated taxable income in the fiscal years 2018 to 2021 and 2023. The Company expects to continue to generate taxable income in the U.S. during the foreseeable future. ​ Under the provision of the Internal Revenue Code, the U.S. net operating losses carried forward may become subject to an annual limitation in the event of certain cumulative exchange in the ownership interest of significant shareholders over a three-year period in excess of 50 percent, as defined under Section 382 and 383 of the Internal Revenue Code. This could limit the amount of tax attributes that can be utilized annually to offset future taxable income or tax liabilities. The amount of the annual limitation is determined based on the value of the Company immediately prior to the ownership change. Subsequent ownership changes may further affect the limitation. ​ The fiscal periods from 2020 are still open for inspection by the Internal Revenue Service (“IRS”). To the extent the Company has tax attribute carryforwards, the tax years in which the attribute was generated may still be adjusted upon examination by the IRS or Massachusetts Department of Revenue to the extent utilized in a future period. The Company is currently not under examination by the IRS for any tax years. ​ 150 ​ Table of Contents France ​ The French corporate tax rate for fiscal year 2023 was 25.0 %. In addition, the Company is subject to a surcharge of 3.3 % of the 25.0 % standard corporate tax rate resulting in a combined rate of 25.8 %. ​ The Company’s French operations have incurred losses since incorporation and are expected to continue incurring tax losses for the foreseeable future. The French operations as of December 31, 2023 have an estimated $ 39.6 million ($ 23.3 million as of December 31, 2022) of net operating losses that are available for carry forward indefinitely. The Company recorded a partial valuation allowance during the year ended December 31, 2023. No such valuation allowance was recorded in the years ended December 31, 2022 and 2021. The Company evaluates all positive and negative evidence including future income from reversing taxable temporary differences (particularly from reversing the deferred tax liability related to the acquired IPR&D intangible asset), projected future taxable income and tax-planning strategies in making this assessment. ​ ​ 21. Basic and diluted earnings per share ​ Basic net (loss) / income per ordinary share is computed by dividing net (loss) / income for the period by the weighted average number of ordinary shares outstanding during the period. Diluted earnings per ordinary share are calculated by adjusting the weighted average number of ordinary shares outstanding, assuming conversion of all potentially dilutive ordinary shares. For the year ended December 31, 2021, dilutive net income / (loss) per ordinary share is computed using the treasury method. As the Company has incurred a loss in the years ended December 31, 2023 and December 31, 2022, all potentially dilutive ordinary shares for these years would have an antidilutive effect, if converted, and thus have been excluded from the computation of loss per share for the years ended December 31, 2023 and December 31, 2022. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ 2023 ​ 2022 ​ 2021 ​ ​ (in thousands, except share amounts) Numerator: ​ ​ ​ ​ ​ ​ ​ ​ ​ Net (loss) / income attributable to ordinary shares ​ $ ( 308,478 ) ​ $ ( 126,789 ) ​ $ 329,589 ​ ​ ​ ( 308,478 ) ​ ​ ( 126,789 ) ​ ​ 329,589 Denominator: ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted-average number of ordinary shares outstanding - basic ​ ​ 47,670,986 ​ ​ 46,735,045 ​ ​ 45,986,467 Stock options under 2014 Plans and previous plan ​ ​ — ​ ​ — ​ ​ 746,044 Non-vested RSUs and PSUs ​ ​ — ​ ​ — ​ ​ 107,162 Employee share purchase plan ​ ​ — ​ ​ — ​ ​ 1,299 Weighted-average number of ordinary shares outstanding - diluted ​ ​ 47,670,986 ​ ​ 46,735,045 ​ ​ 46,840,972 ​ The following table presents ordinary share equivalents that were excluded from the calculation of diluted net income / (loss) per ordinary share for the years ended December 31, 2023, 2022 and 2021 as the effect of their inclusion would have been anti-dilutive: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ 2023 ​ 2022 ​ 2021 Anti-dilutive ordinary share equivalents ​ ​ ​ ​ ​ ​ ​ ​ ​ Stock options under 2014 Plans and previous plan ​ ​ 4,974,030 ​ ​ 4,237,917 ​ ​ 2,576,281 Non-vested RSUs and PSUs ​ ​ 2,486,919 ​ ​ 2,219,464 ​ ​ 1,236,385 ESPP ​ ​ 3,640 ​ ​ 1,048 ​ ​ 1,842 Total anti-dilutive ordinary share equivalents ​ ​ 7,464,589 ​ ​ 6,458,429 ​ ​ 3,814,508 ​ The anti-dilutive ordinary shares are presented without giving effect to the application of the treasury method or exercise prices that exceeded the price of the Company’s ordinary shares as of December 31, 2023 and December 31, 2022. ​ ​ ​ 151 ​ Table of Contents 22. Commitments and contingencies ​ In the course of its business, the Company enters as a licensee into contracts with other parties regarding the development and marketing of its pipeline products. Among other payment obligations, the Company is obligated to pay royalties to the licensors based on future sales levels and milestone payments whenever specified development, regulatory and commercial milestones are met. As both future sales levels and the timing and achievement of milestones are uncertain, the financial effect of these agreements cannot be estimated reliably. The Company also has obligations to make future payments that become due and payable upon the collection of milestone payments from CSL Behring. The achievement and timing of these milestones is not fixed and determinable. Relevant commitments and contingencies are further discussed in other sections of this form 10-K, such as, Note 3 “ uniQure France SAS transaction ” and Note 5 “ Collaboration arrangements and concentration of credit risk ”, amongst others. ​ 23. Related party transaction ​ None. ​ ​ 24. Subsequent events ​ None. ​ ​ 152 ​ Table of Contents EXHIBIT INDEX ​ Exhibit No. Description 2.1† ​ Sale and Purchase Agreement, executed June 21, 2021, by and between uniQure N.V. and Corlieve Therapeutics SAS (incorporated by reference to Exhibit 2.1 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2021 filed with the SEC on July 26, 2021). 3.1 ​ Amended Articles of Association of the Company (incorporated by reference to Exhibit 3.1 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2021 filed with the SEC on July 26, 2021). 4.1 * Description of the Registrant’s Securities Registered Pursuant to Section 12 of the Securities Exchange Act of 1934. 10.1 t ​ 2014 Share Incentive Plan (incorporated by reference to Exhibit 4.3 of the Company's registration statement on Form S-8 (file no. 333-225629) filed with the SEC on June 14, 2018). 10.6 t ​ Employment Agreement dated December 9, 2014 between uniQure, Inc. and Matthew Kapusta (incorporated by reference to Exhibit 10.6 of the Company's annual report on Form 10-K (file no. 001-36294) for the year ended December 31, 2016 filed with the SEC on March 15, 2017). 10.7 t ​ Amendment to the Employment Agreement between uniQure, Inc. and Matthew Kapusta, dated March 14, 2017 (incorporated by reference to Exhibit 10.7 of the Company's annual report on Form 10-K (file no. 001-36294) for the year ended December 31, 2016 filed with the SEC on March 15, 2017). 10.8 t ​ Amendment to the Employment Agreement between uniQure, Inc. and Matthew Kapusta, dated October 26, 2017 (incorporated by reference to Exhibit 10.1 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ended September 30, 2017 filed with the SEC on November 1, 2017). 10.18 ​ Lease relating to 113 Hartwell Avenue, Lexington, Massachusetts, dated as of July 24, 2013, by and between uniQure Inc. and King 113 Hartwell LLC (incorporated by reference to Exhibit 10.28 of the Company's registration statement on Form F-1 (file no. 333-193158) filed with the SEC on January 2, 2014). 10.19 ​ Business Acquisition Agreement, dated as of February 16, 2012, by and among Amsterdam Molecular Therapeutics (AMT) Holding N.V., the Company and the other Parties listed therein (incorporated by reference to Exhibit 10.29 of the Company's registration statement on Form F-1 (file no. 333-193158) filed with the SEC on January 2, 2014). 10.20 ​ Deed of Assignment of Certain Assets and Liabilities of Amsterdam Molecular Therapeutics (AMT) Holding N.V., dated as of April 5, 2012, by and among Amsterdam Molecular Therapeutics (AMT) Holding B.V., Amsterdam Molecular Therapeutics (AMT) Holding IP B.V. and Amsterdam Molecular Therapeutics (AMT) Holding N.V. (incorporated by reference to Exhibit 10.30 of the Company's registration statement on Form F-1 (file no. 333-193158) filed with the SEC on January 2, 2014). 10.21 ​ Agreement for Transfer of Certain Assets and Liabilities of Amsterdam Molecular Therapeutics (AMT) Holding N.V., dated as of February 16, 2012, by and among Amsterdam Molecular Therapeutics (AMT) Holding B.V., Amsterdam Molecular Therapeutics (AMT) Holding IP B.V. and Amsterdam Molecular Therapeutics (AMT) Holding N.V. (incorporated by reference to Exhibit 10.31 of the Company's registration statement on Form F-1 (file no. 333-193158) filed with the SEC on January 2, 2014). 10.29† ​ Investor Agreement by and between uniQure Biopharma B.V. and Bristol-Myers Squibb Company dated April 6, 2015 (incorporated by reference to Exhibit 4.32 of the Company's annual report on Form 20-F for the year ended December 31, 2014 (file no. 001-36294) filed with the SEC on April 7, 2015). 10.32 ​ Lease relating to Paasheuvelweg 25, dated as of March 7, 2016, by and between 52 IFH GmbH & Co. KG and uniQure biopharma B.V. (incorporated by reference to Exhibit 10.36 of the Company's annual report on Form 10-K (file no. 001-36294) for the year ended December 31, 2016 filed with the SEC on March 15, 2017). 153 ​ Table of Contents 10.37† ​ Assignment and License Agreement dated April 17, 2017 between Professor Paolo Simioni and uniQure biopharma B.V. (incorporated by reference to Exhibit 10.1 of the Company’s current report on Form 8-K (file no. 001-36294) filed with the SEC on October 19, 2017). 10.40 ​ First Amendment Lease relating to 113 Hartwell Avenue, Lexington, Massachusetts, dated as of July 24, 2013, by and between the Company and King113 Hartwell LLC (incorporated by reference to Exhibit 10.1 of the Company's current report on form 8-K (file no. 001-36294) filed with the SEC on November 15, 2018). 10.41t ​ Employee Share Purchase Plan (incorporated by reference to Exhibit 4.2 of the Company's registration statement on Form S-8 (file no. 333-225629) filed with the SEC on June 14, 2018). 10.42 ​ Second Amendment Lease relating to 113 Hartwell Avenue, Lexington Massachusetts, dated as of June 17, 2019, by and between the Company and King 113 Hartwell LLC (incorporated by reference to Exhibit 10.42 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2019 filed with the SEC on July 29, 2019). 10.53† ​ Commercialization and License Agreement by and between uniQure biopharma B.V. and CSL Behring LLC dated June 24, 2020 (incorporated by reference to Exhibit 10.1 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2020 filed with the SEC on July 30, 2020). 10.56t ​ Employment Agreement, executed September 14, 2020, by and between uniQure Inc. and Ricardo Dolmetsch (incorporated by reference to Exhibit 10.3 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ended September 30, 2020 filed with the SEC on October 27, 2020). 10.60t ​ Amended and Restated 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.1 of the Company’s current report on Form 8-K (file no. 001-36294) filed with the SEC on November 17, 2023). 10.61t ​ Employment Agreement, effective May 17, 2021, by and between uniQure biopharma B.V. and Pierre Caloz (incorporated by reference to Exhibit 10.1 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2021 filed with the SEC on July 26, 2021). 10.62t ​ Equity Side Letter, effective May 17, 2021, by and between uniQure N.V. and Pierre Caloz (incorporated by reference to Exhibit 10.2 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2021 filed with the SEC on July 26, 2021). 10.63t ​ Amended and Restated Employment Agreement, effective June 15, 2021, by and between uniQure biopharma B.V. and Christian Klemt (incorporated by reference to Exhibit 10.3 of the Company’s quarterly report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2021 filed with the SEC on July 26, 2021). 10.65t ​ Form of Share Option Agreement, effective December 8, 2021, under the 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.65 of the Company’s annual report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 10.66t ​ Form of Restricted Stock Unit Award, effective December 8, 2021, under the 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.66 of the Company’s annual report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 10.67†t ​ Form of Performance Stock Unit Award, effective December 8, 2021 under the 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.67 of the Company’s annual report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 10.68† ​ Third Amended and Restated Loan and Security Agreement as of December 15, 2021, by and among uniQure biopharma B.V., uniQure Inc., uniQure IP B.V., the Company and Hercules Capital Inc (incorporated by reference to Exhibit 10.68 of the Company’s annual report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 10.69† ​ Lease Agreement relating to 20 Maguire Road, Lexington, Massachusetts, dated as of December 22, 2021, by and between uniQure Inc. and G&I IX/GP4 20 Maguire LLC (incorporated by reference to Exhibit 10.69 of the Company’s annual report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 154 ​ Table of Contents 10.70† ​ Lease Agreement relating to 91 Hartwell Avenue, Lexington, Massachusetts, dated as of February 1, 2022, by and between uniQure Inc. and NRL 91 Hartwell LLC (incorporated by reference to Exhibit 10.70 of the Company’s annual report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 10.71† ​ Amendment No. 1 to Third Amended and Restated Loan and Security Agreement, dated of May 12, 2023, by and among uniQure biopharma, B.V., uniQure, Inc., uniQure IP B.V., the Company and Hercules Capital, Inc. (incorporated by reference to Exhibit 10.1 of the Company’s quarterly report on Form 10-Q for the period ended June 30, 2023 (file no. 001-36294) filed with the SEC on August 1, 2023). 10.72† ​ Royalty Purchase Agreement, dated May 12, 2023, by and between uniQure biopharma B.V. and HemB SPV, L.P. (incorporated by reference to Exhibit 10.2 of the Company’s quarterly report on Form 10-Q for the period ended June 30, 2023 (file no. 001-36294) filed with the SEC on August 1, 2023). 10.73t ​ Termination and Consulting Agreement, effective October 4, 2023, by and between uniQure Inc. and Ricardo Dolmetsch, Ph.D. (incorporated by reference to Exhibit 10.1 of the Company’s quarterly report on Form 10-Q for the period ended September 30, 2023 (file no. 001-36294) filed with the SEC on November 7, 2023). 10.74t* ​ Employment Agreement dated July 30, 2021 between Corlieve Therapeutics AG and Richard Porter. 10.75t* ​ First Amended Employment Agreement dated April 1, 2022 between Corlieve Therapeutics AG and Richard Porter. 10.76t* ​ Letter Agreement dated October 5, 2023, by and between Richard Porter and Corlieve Therapeutics AG. 10.77t* ​ Employment Agreement dated June 13, 2023 between uniQure, Inc. and Jeannette Potts. 14.1* ​ Code of Ethics. 21.1* ​ Subsidiaries of the Company. 23.1* ​ Consent of Independent Registered Public Accounting Firm – KPMG Accountants N.V. 24.1* ​ Power of Attorney (incorporated by reference to the signature page of this Annual Report on Form 10-K). 31.1* ​ Rule 13a-14(a)/15d-14(a) Certification of Chief Executive Officer. 31.2* ​ Rule 13a-14(a)/15d-14(a) Certification of Chief Financial Officer. 32.1* ​ Certification of Principal Executive Officer and Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. 97.1* ​ uniQure N.V. Compensation Clawback Policy. 101* ​ The following materials from the Company’s Annual Report on Form 10-K for the year ended December 31, 2023, formatted in Inline XBRL (eXtensible Business Reporting Language): (i) Consolidated Balance Sheets, (ii) Consolidated Statements of Operations and Comprehensive Income (Loss), (iii) Consolidated Statements of Shareholders’ Equity, (iv) Consolidated Statements of Cash Flows and (v) Notes to Consolidated Financial Statements. 104* ​ The cover page from the Company’s Annual Report on Form 10-K for the year ended December 31, 2023, has been formatted in Inline XBRL. ​ ​ † Confidential treatment requested as to certain portions, which portions have been omitted and filed separately with the Securities and Exchange Commission ​ * Filed herewith ​ t Indicates a management contract or compensatory plan or arrangement. ​ ​ 155 ​ Table of Contents SIGNATURES ​ Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized. ​ ​ ​ ​ ​ UNIQURE N.V. ​ ​ ​ Date: February 28, 2024 By: /s/ MATTHEW KAPUSTA ​ ​ Matthew Kapusta ​ ​ Chief Executive Officer (Principal Executive Officer) ​ ​ ​ Date: February 28, 2024 By: /s/ CHRISTIAN KLEMT ​ ​ Christian Klemt ​ ​ Chief Financial Officer (Principal Financial Officer and Principal Accounting Officer) ​ POWER OF ATTORNEY ​ KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints Matthew Kapusta and Christian Klemt, jointly and severally, his or her attorney-in-fact, with the power of substitution, for him or her in any and all capacities, to sign any amendments to this Annual Report on Form 10-K and to file the same, with exhibits thereto and other documents in connection therewith, with the Securities and Exchange Commission, hereby ratifying and confirming all that each of said attorneys-in-fact, or his or her substitute or substitutes, may do or cause to be done by virtue hereof. ​ Pursuant to the requirements of the Securities Exchange Act of 1934, this Annual Report on Form 10-K has been signed below by the following persons on behalf of the Registrant and in the capacities and on the dates indicated. ​ Signatures Title Date ​ ​ ​ ​ ​ /s/ MATTHEW KAPUSTA ​ Chief Executive Officer and Director (Principal Executive Officer) ​ February 28, 2024 Matthew Kapusta ​ ​ ​ ​ ​ ​ ​ /s/ CHRISTIAN KLEMT ​ Chief Financial Officer (Principal Financial Officer and Principal Accounting Officer) ​ February 28, 2024 Christian Klemt ​ ​ ​ ​ ​ ​ ​ /s/ MADHAVAN BALACHANDRAN ​ Director ​ February 28, 2024 Madhavan Balachandran ​ ​ ​ ​ ​ ​ ​ /s/ ROBERT GUT ​ Director ​ February 28, 2024 Robert Gut ​ ​ ​ ​ ​ ​ ​ /s/ RACHELLE JACQUES ​ Director ​ February 28, 2024 Rachelle Jacques ​ ​ ​ ​ ​ ​ ​ /s/ JACK KAYE ​ Director ​ February 28, 2024 Jack Kaye ​ ​ ​ ​ ​ ​ ​ /s/ DAVID MEEK ​ Director ​ February 28, 2024 David Meek ​ ​ ​ ​ ​ ​ ​ /s/ LEONARD POST ​ Director ​ February 28, 2024 Leonard Post ​ ​ ​ ​ ​ ​ ​ /s/ PAULA SOTEROPOULOS ​ Director ​ February 28, 2024 Paula Soteropoulos ​ ​ ​ ​ ​ ​ ​ ​ ​ /s/ JEREMY P. SPRINGHORN ​ Director ​ February 28, 2024 Jeremy P. Springhorn ​ ​ ​ ​ ​ ​ 156 ​