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Form10-Q (Mark One) ☒QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the Quarterly Period EndedSeptember 30,2025 OR ☐TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF SECURITIES EXCHANGE ACT OF 1934 For the transition period from _____ to _____ Commission file number000-19125 Ionis Pharmaceuticals, Inc. (Exact name of Registrant as specified in its charter) Delaware33-0336973(State or other jurisdiction of incorporation or organization)(IRS Employer Identification No.) 2855 Gazelle Court,Carlsbad,California92010(Address of Principal Executive Offices)(Zip Code) 760-931-9200(Registrant’s telephone number, including area code) Securities registered pursuant to Section 12(b) of the Act: Title of each classTrading symbolName of each exchange on whichregisteredCommon Stock, $.001 Par Value“IONS”TheNasdaqStock Market LLC Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of theSecurities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file suchreports), and (2) has been subject to such filing requirements for the past 90 days.Yes☒No☐ Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submittedand posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter periodthat the registrant was required to submit such files).Yes☒No☐ Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, smallerreporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smallerreporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act. Large Accelerated Filer☒ Non-accelerated Filer☐ If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period forcomplying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act.☐ Indicate by check mark whether the registrant is a shell company (as defined in Rule 12(b)-2 of the Securities Exchange Act of1934). Yes☐No☒ The number of shares of voting common stock outstanding as of October 23, 2025 was161,974,393. IONIS PHARMACEUTICALS, INC.FORM 10-QINDEX PART IFINANCIAL INFORMATIONITEM 1:Financial Statements:Condensed Consolidated Balance Sheetsas of September 30, 2025 (unaudited) and December 31, 20243Condensed Consolidated Statements of Operationsfor the three and nine months endedSeptember 30, 2025 and2024 (unaudited)4Condensed Consolidated Statements of Comprehensive Lossfor the three and nine months ended September 30,2025 and 2024 (unaudited)5Condensed Consolidated Statements of Stockholders’ Equityfor the three and nine months ended September 30,2025 and 2024 (unaudited)6Condensed Consolidated Statements of Cash Flowsfor the nine months ended September 30, 2025 and 2024(unaudited)8Notes to Condensed Consolidated Financial Statements (unaudited)9ITEM 2:Management’s Discussion and Analysis of Financial Condition and Results of Operations:Overview23Critical Accounting Estimates25Results of Operations26Liquidity and Capital Resources31ITEM 3:Quantitative and Qualitative Disclosures about Market Risk33ITEM 4:Controls and Procedures33PART IIOTHER INFORMATION34ITEM 1:Legal Proceedings34ITEM 1A:Risk Factors34ITEM 2:Unregistered Sales of Equity Securities and Use of Proceeds52ITEM 3:Default upon Senior Securities52ITEM 4:Mine Safety Disclosures52ITEM 5:Other Information52ITEM 6:Exhibits53SIGNATURES54TRADEMARKS “Ionis,” the Ionis logo, and other trademarks or service marks of Ionis Pharmaceuticals, Inc. appearing in this report are theproperty of Ionis Pharmaceuticals, Inc. “Akcea,” the Akcea logo, and other trademarks or service marks of Akcea Therapeutics, Inc.appearing in this report are the property of Akcea Therapeutics, Inc., Ionis’ wholly owned subsidiary. This report contains additional tradenames, trademarks and service marks of others, which are the property of their respective owners. Solely for convenience, trademarksand trade names referred to in this report may appear without the ® or TM symbols. IONIS PHARMACEUTICALS, INC.CONDENSED CONSOLIDATED BALANCE SHEETS(in thousands, except share data) IONIS PHARMACEUTICALS, INC.CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS(in thousands, except per share amounts)(Unaudited) IONIS PHARMACEUTICALS, INC.CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE LOSS(in thousands)(Unaudited) IONIS PHARMACEUTICALS, INC.NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTSSeptember 30, 2025(Unaudited) 1.Organization and Basis of Presentation Organization and Business Activity We incorporated in California on January 10, 1989. In conjunction with our initial public o