Item 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES

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Item 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES

(a)(1) The Financial Statements required to be filed by Items 8 and 15(c) of Form 10-K, and filed herewith, are as

follows:

Page Number in this Form 10-K
Report of Independent Registered Public Accounting Firm (PCAOB ID: 42) .......................................................F-1
Consolidated Statements of Income (Loss) .........................................................................................................................F-3
Consolidated Statements of Comprehensive Income (Loss) ...............................................................................................F-4
Consolidated Balance Sheets ...............................................................................................................................................F-5
Consolidated Statements of Shareholders’ Equity ...............................................................................................................F-6
Consolidated Statements of Cash Flows ..............................................................................................................................F-7
Notes to Consolidated Financial Statements ........................................................................................................................F-8

(a)(2) Financial Statement Schedules have been omitted because they are either not applicable or the required

information is included in the consolidated financial statements or notes thereto listed in (a)(1) above.

(a)(3) Exhibits.

The following is a list of exhibits filed as part of this Annual Report on Form 10-K.

Exhibit NumberExhibit DescriptionFiled with this reportIncorporated by Reference herein from—Form or ScheduleFiling Date/ Period CoveredSEC File/ Reg. Number
Governance Documents
3.1Restated Articles of Organization of Vertex Pharmaceuticals Incorporated, as amended.X
3.2Amended and Restated By-Laws of Vertex Pharmaceuticals Incorporated.10-K (Exhibit 3.2)February 13, 2025000-19319
Stock Certificate
4.1Specimen Stock Certificate.10-K (Exhibit 4.1)February 15, 2018000-19319
4.2Description of Securities.10-K (Exhibit 4.2)February 13, 2025000-19319
Collaboration Agreement
10.1Research, Development and Commercialization Agreement, dated as of May 24, 2004, between Vertex Pharmaceuticals Incorporated and Cystic Fibrosis Foundation Therapeutics Incorporated.†10-Q (Exhibit 10.1)November 3, 2021000-19319
10.2Amendment No. 1 to Research, Development and Commercialization Agreement, dated as of January 6, 2006, between Vertex Pharmaceuticals Incorporated and Cystic Fibrosis Foundation Therapeutics Incorporated.†10-Q (Exhibit 10.2)November 3, 2021000-19319
10.3Amendment No. 2 to Research, Development and Commercialization Agreement, dated as of March 17, 2006, between Vertex Pharmaceuticals Incorporated and Cystic Fibrosis Foundation Therapeutics Incorporated.10-Q/A (Exhibit 10.6)August 19, 2011000-19319
10.4Amendment No. 5 to Research, Development and Commercialization Agreement, effective as of April 1, 2011, between Vertex Pharmaceuticals Incorporated and Cystic Fibrosis Foundation Therapeutics Incorporated.†10-Q (Exhibit 10.3)November 3, 2021000-19319
10.5Amendment No. 7 to Research, Development and Commercialization Agreement, dated October 13, 2016, between Vertex Pharmaceuticals Incorporated and Cystic Fibrosis Foundation Therapeutics Incorporated.†10-Q (Exhibit 10.4)November 3, 2021000-19319
Exhibit NumberExhibit DescriptionFiled with this reportIncorporated by Reference herein from—Form or ScheduleFiling Date/ Period CoveredSEC File/ Reg. Number
10.6Amended and Restated Joint Development and Commercialization Agreement, dated April 16, 2021, between Vertex Pharmaceuticals Incorporated, Vertex Pharmaceuticals (Europe) Limited and CRISPR Therapeutics AG, CRISPR Therapeutics Limited, CRISPR Therapeutics, Inc., TRACR Hematology Ltd.†10-Q (Exhibit 10.1)July 30, 2021000-19319
10.7Amendment No. 1 to Amended and Restated Joint Development and Commercialization Agreement, dated December 12, 2023, between Vertex Pharmaceuticals Incorporated, Vertex Pharmaceuticals (Europe) Limited and CRISPR Therapeutics AG, CRISPR Therapeutics Limited, CRISPR Therapeutics, Inc., TRACR Hematology Ltd.†10-K (Exhibit 10.7)February 15, 2024000-19319
Leases
10.8Lease, dated May 5, 2011, between Fifty Northern Avenue LLC and Vertex Pharmaceuticals Incorporated.†10-Q (Exhibit 10.2)July 30, 2021000-19319
10.92024 Amendment to the Lease (50 Northern Avenue), dated August 15, 2024, between Vertex Pharmaceuticals Incorporated and SNH Seaport LLC. †10-Q (Exhibit 10.1)November 5, 2024000-19319
10.10Lease, dated May 5, 2011, between Eleven Fan Pier Boulevard LLC and Vertex Pharmaceuticals Incorporated.†10-Q (Exhibit 10.3)July 30, 2021000-19319
10.112024 Amendment to Lease (11 Fan Pier Boulevard), dated August 15, 2024, between Vertex Pharmaceuticals Incorporated and SNH Seaport LLC.†10-Q (Exhibit 10.2)November 5, 2024000-19319
Financing Agreements
10.12Credit Agreement, dated as of July 1, 2022, by and among Vertex Pharmaceuticals Incorporated, Bank of America, N.A. and the other lenders party thereto.10-Q (Exhibit 10.1)August 5, 2022000-19319
10.13First Amendment to Credit Agreement, dated June 20, 2024 by and between Vertex Pharmaceuticals Incorporated and Bank of America N.A.10-Q (Exhibit 10.1)August 2, 2024000-19319
Equity Plans
10.14Amended and Restated 2006 Stock and Option Plan.*10-Q (Exhibit 10.1)October 25, 2018000-19319
10.15Form of Stock Option Agreement under Amended and Restated 2006 Stock and Option Plan (granted on or after July 30, 2013).*10-K (Exhibit 10.20)February 13, 2015000-19319
10.16Amended and Restated 2013 Stock and Option Plan.*DEF 14A (Appendix A)April 7, 2022000-19319
10.17Form of Non-Qualified Stock Option Agreement under 2013 Stock and Option Plan.*10-K (Exhibit 10.17)February 13, 2015000-19319
10.18Form of Restricted Stock Unit Agreement under 2013 Stock and Option Plan (U.S.).*10-K (Exhibit 10.25)February 16, 2016000-19319
10.19Form of Restricted Stock Unit Agreement under 2013 Stock and Option Plan (International).*10-K (Exhibit 10.19)February 13, 2015000-19319
10.20Form of Restricted Stock Unit Agreement Under 2013 Stock and Option Plan.*10-K (Exhibit 10.17)February 13, 2020000-19319
10.21Form of Restricted Stock Unit Agreement under 2013 Stock and Option Plan (granted on or after January 1, 2025).*10-K (Exhibit 10.21)February 13, 2025000-19319
10.22Form of Restricted Stock Unit Agreement (with performance conditions) under 2013 Stock and Option Plan.*10-K (Exhibit 10.22)February 13, 2025000-19319
10.23Non-Employee Director Deferred Compensation Plan.*10-K (Exhibit 10.27)February 16, 2016000-19319
10.24Vertex Pharmaceuticals Incorporated Employee Stock Purchase Plan.*DEF 14A (Appendix B)April 26, 2019000-19319
Agreements with Executive Officers and Directors
10.25Employment Agreement, dated as of April 1, 2020, by and between Vertex Pharmaceuticals Incorporated and Jeffrey M. Leiden, M.D., Ph.D.*8-K (Exhibit 10.1)April 1, 2020000-19319
10.26Amendment No. 1 to Employment Agreement, between Jeffrey M. Leiden and Vertex Pharmaceuticals Incorporated, dated as of February 7, 2022.*10-K (Exhibit 10.24)February 9, 2022000-19319
10.27Amendment No. 2 to Employment Agreement, between Jeffrey M. Leiden and Vertex Pharmaceuticals Incorporated, dated as of February 8, 2023*10-K (Exhibit 10.23)February 10, 2023000-19319
Exhibit NumberExhibit DescriptionFiled with this reportIncorporated by Reference herein from—Form or ScheduleFiling Date/ Period CoveredSEC File/ Reg. Number
10.28Amendment No.3 to Employment Agreement, between Jeffrey M. Leiden and Vertex Pharmaceuticals Incorporated, dated as of November 1, 2024.*10-Q (Exhibit 10.3)November 5, 2024000-19319
10.29Employee Non-disclosure, Non-competition and Inventions Agreement between Jeffrey M. Leiden and Vertex Pharmaceuticals Incorporated, dated December 14, 2011.*10-K (Exhibit 10.35)February 22, 2012000-19319
10.30Employment Agreement, dated as of July 24, 2019, between Vertex Pharmaceuticals Incorporated and Reshma Kewalramani.*8-K (Exhibit 10.1)July 25, 2019000-19319
10.31Change of Control Agreement, dated as of July 24, 2019, between Vertex Pharmaceuticals Incorporated and Reshma Kewalramani.*8-K (Exhibit 10.2)July 25, 2019000-19319
10.32Employment Agreement, dated as of August 27, 2012, between Vertex Pharmaceuticals Incorporated and Stuart Arbuckle.*10-Q (Exhibit 10.1)November 6, 2012000-19319
10.33Change of Control Agreement, dated as of August 27, 2012, between Vertex Pharmaceuticals Incorporated and Stuart Arbuckle.*10-Q (Exhibit 10.2)November 6, 2012000-19319
10.34Employment Agreement, dated as of December 12, 2014, between Vertex Pharmaceuticals Incorporated and David Altshuler.*10-K (Exhibit 10.34)February 16, 2016000-19319
10.35Change of Control Agreement, dated as of December 10, 2014, between Vertex Pharmaceuticals Incorporated and David Altshuler.*10-K (Exhibit 10.35)February 16, 2016000-19319
10.36Third Amended and Restated Employment Agreement, dated as of February 26, 2013, between Vertex Pharmaceuticals Incorporated and Amit Sachdev.*10-K (Exhibit 10.42)February 23, 2017000-19319
10.37Third Amended and Restated Change of Control Agreement, dated as of February 26, 2013, between Vertex Pharmaceuticals Incorporated and Amit Sachdev.*10-K (Exhibit 10.43)February 23, 2017000-19319
10.38Employment Agreement, dated February 7, 2025, by and between Vertex Pharmaceuticals Incorporated and Charles F. Wagner, Jr.*10-Q (Exhibit 10.1)May 6, 2025000-19319
10.39Change of Control Agreement, dated as of February 7, 2025, by and between Vertex Pharmaceuticals Incorporated and Charles F. Wagner, Jr.*10-K (Exhibit 10.39)February 13, 2025000-19319
10.40Employment Agreement, dated August 1, 2020, by and between Vertex Pharmaceuticals Incorporated and Nia Tatsis.*10-K (Exhibit 10.36)February 9, 2022000-19319
10.41Change of Control Agreement, dated August 1, 2020, by and between Vertex Pharmaceuticals Incorporated and Nia Tatsis.*10-K (Exhibit 10.37)February 9, 2022000-19319
10.42Employment Agreement, dated October 3, 2022, by and between Vertex Pharmaceuticals Incorporated and Carmen Bozic.*X
10.43Change of Control Agreement, dated October 3, 2022, by and between Vertex Pharmaceuticals Incorporated and Carmen Bozic.*X
10.44Vertex Pharmaceuticals Employee Compensation Plan.*X
10.45Vertex Pharmaceuticals Non-Employee Board Compensation.*10-K (Exhibit 10.43)February 13, 2025000-19319
Insider Trading Policy
19.1Vertex Pharmaceuticals Incorporated Insider Trading Policy. *10-K (Exhibit 19.1)February 13, 2025000-19319
Subsidiaries
21.1Subsidiaries of Vertex Pharmaceuticals Incorporated.X
Consent
23.1Consent of Independent Registered Public Accounting Firm, Ernst & Young LLP.X
Certifications
31.1Certification of the Chief Executive Officer under Section 302 of the Sarbanes- Oxley Act of 2002.X
31.2Certification of the Chief Financial Officer under Section 302 of the Sarbanes- Oxley Act of 2002.X
32.1Certification of the Chief Executive Officer and the Chief Financial Officer under Section 906 of the Sarbanes-Oxley Act of 2002.X
Clawback Policy
97.1Policy Relating to Recovery of Erroneously Awarded Compensation10-K (Exhibit 97.1)February 15, 2024000-19319
Exhibit NumberExhibit DescriptionFiled with this reportIncorporated by Reference herein from—Form or ScheduleFiling Date/ Period CoveredSEC File/ Reg. Number
101.INSXBRL InstanceX
101.SCHXBRL Taxonomy Extension SchemaX
101.CALXBRL Taxonomy Extension CalculationX
101.LABXBRL Taxonomy Extension LabelsX
101.PREXBRL Taxonomy Extension PresentationX
101.DEFXBRL Taxonomy Extension DefinitionX
104Cover Page Interactive Data File––the cover page interactive data file does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document.X
*Management contract, compensatory plan or agreement.
†Confidential portions of this document have been redacted according to the applicable rules.

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