Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Form 10-K (Mark One) ☑ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2003 or o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 0-19311 Biogen Idec Inc. (Exact name of registrant as specified in its charter) Delaware 33-0112644 (State or other jurisdiction of (I.R.S. Employer incorporation or organization) Identification No.) 14 Cambridge Center, Cambridge, Massachusetts 02142 (Address of principal executive offices) (Zip code) (617) 679-2000 (Registrant’s telephone number, including area code) Securities registered pursuant to Section 12(b) of the Act: None Securities registered pursuant to Section 12(g) of the Act: Common Stock, $0.0005 par value Series X Junior Participating Preferred Stock Purchase Rights (Title of class) Indicate by check mark whether the Registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the Registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ☑ No o Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of the Registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K. ☑ Indicate by check mark whether the Registrant is an accelerated filer (as defined in Exchange Act Rule 12b-2). Yes ☑ No o The aggregate market value of the Registrant’s Common Stock held by non-affiliates of the Registrant (without admitting that any person whose shares are not included in such calculation is an affiliate) computed by reference to the price at which the common stock was last sold as of the last business day of the Registrant’s most recently completed fiscal quarter was $4,762,181.085. As of February 20, 2004, the Registrant had 331,996,625 shares of Common Stock, $0.0005 par value, issued and outstanding. DOCUMENTS INCORPORATED BY REFERENCE Portions of the definitive Proxy Statement for our 2004 Annual Meeting of Stockholders are incorporated by reference into Part III of this Report. BIOGEN IDEC INC. ANNUAL REPORT ON FORM 10-K For the Fiscal Year Ended December 31, 2003 TABLE OF CONTENTS Page PART I Item 1. Business 1 Overview 1 Our Products and Primary Product Candidates — Table 3 Our Products 4 Our Primary Product Candidates 8 Other Research and Development Programs 10 Research and Development Costs 10 Principal Licensed Products 10 Patents and Other Proprietary Rights 11 Sales, Marketing and Distribution 14 Competition 15 Regulatory 17 Manufacturing and Raw Materials 20 Our Employees 20 Our Executive Officers 21 Forward-Looking Information and Risk Factors That May Affect Future Results 24 Item 2. Properties 33 Item 3. Legal Proceedings 34 Item 4. Submission of Matters to a Vote of Security Holders 36 PART II Item 5. Market for Registrant’s Common Equity and Related Stockholder Matters 37 Item 6. Selected Consolidated Financial Data 38 Item 7. Management’s Discussion and Analysis of Financial Condition and Results of Operations 39 Item 7A. Quantitative and Qualitative Disclosures About Market Risk 60 Item 8. Consolidated Financial Statements and Supplementary Data 60 Item 9. Changes in and Disagreements with Accountants on Accounting and Financial Disclosure 60 Item 9A. Controls and Procedures 60 PART III Item 10. Directors and Executive Officers of the Registrant 61 Item 11. Executive Compensation 61 Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters 61 Item 13. Certain Relationships and Related Transactions 61 Item 14. Principal Accounting Fees and Services 61 PART IV Item 15. Exhibits, Financial Statement Schedules, and Reports on Form 8-K 62 Signatures 68 Consolidated Financial Statements and Schedule F-1 EX-3.1 AMENDED AND RESTATED CERTIFICATE OF INCORP EX-3.2 CERTIFICATE OF AMENDMENT EX-3.3 CERTIFICATE INCREASING THE NUMBER OF SHARES EX-3.4 CERTIFICATE OF AMENDMENT EX-3.5 BYLAWS EX-3.6 AMENDMENT TO BYLAWS DATED AS OF 12-21-2001 EX-3.7 AMENDMENT TO BYLAWS DATED AS OF 11-12-2003 EX-4.2 SPECIMEN COMMON STOCK CERTIFICATE EX-10.13 VOLUNTARY EXECUTIVE SUP. SAVINGS PLAN EX-10.28 VOLUNTARY BOARD OF DIR SAVINGS PLAN EX-10.29 EXECUTIVE SEVERANCE POLICY EX-10.34 FOURTH AMENDMENT TO AGREEMENT EX-10.35 FIFTH AMENDMENT TO AGREEMENT EX-10.36 FIRST AMENDMENT TO LEASE DATED 10-1-1999 EX-10.37 SECOND AMENDMENT TO LEASE DATED 6-16-2000 EX-10.38 THIRD AMENDMENT TO LEASE DATED 10-13-2000 EX-10.39 FIRST AMENDMENT TO LEASE DATED 11-9-1992 EX-10.40 LEASE AMENDMENT DATED 12-30-1994 EX-10.41 LEASE AGREEMENT EX-10.42 FIRST AMENDMENT TO LEASE DATED 9-12-2000 EX-10.43 SECOND AMENDMENT TO LEASE DATED 11-1-2000 EX-10.44 SINGLE-TENANT FULLY-NET LEASE AGREEMENT EX-10.45 FORM OF LETTER AGREEMENT EX-12.1 COMPUTATION OF RATIO OF EARNINGS EX-21.1 SUBSIDIARIES Consent of PricewaterhouseCoopers LLP EX-23.2 CONSENT OF KPMG LLP. EX-31.1 CEO CERTIFICATION EX-31.2 CFO CERTIFICATION EX-32.1 CERTIFICATION PERSUANT TO SECTION 906 i Table of Contents PART I Item 1. Business. Overview In November 2003, Biogen, Inc. and IDEC Pharmaceuticals Corporation merged under the name Biogen Idec Inc., bringing together the complementary strengths of each company. Biogen Idec creates new standards of care in oncology and immunology. As a global leader in the development, manufacturing, and commercialization of novel therapies, we transform scientific discoveries into advances in human healthcare. We currently have four commercial products: AVONEX® (Interferon beta-1a) for the treatment of relapsing multiple sclerosis, also known as MS, RITUXAN® (rituximab) and ZEVALIN® (ibritumomab tiuxetan), both of which treat certain B-cell non- Hodgkin’s lymphomas, also referred to as B-cell NHLs, and AMEVIVE® (alefacept) for the treatment of adult patients with moderate-to-severe chronic plaque psoriasis who are candidates for systemic therapy or phototherapy. We also receive revenues from royalties on sales by our licensees of a number of products covered under patents that we control including sales of RITUXAN outside the U.S. In addition, we have a pipeline of development stage products and a number of research programs in our core therapeutic areas and in other areas of interest. AVONEX is the most prescribed therapeutic product in MS worldwide. Globally over 125,000 patients have chosen AVONEX as their treatment of choice. In 2003, sales of AVONEX generated worldwide revenues of $1.16 billion as compared to revenues of $1.03 billion from sales of AVONEX in 2002. RITUXAN, the first monoclonal antibody approved by the U.S. Food and Drug Administration for a cancer therapy indication, is currently marketed and sold worldwide for the treatment of various B-cell NHLs. We market RITUXAN in the U.S. in collaboration with Genentech, Inc. All U.S. sales of RITUXAN are recognized by Genentech and we record our share of the pretax copromotion profits on a quarterly basis. In 2003, RITUXAN generated U.S. net sales of $1.36 billion of which we recorded $419.2 million as our share of copromotion profits as compared to U.S. net sales of $1.08 billion in 2002 of which we recorded $324.5 million as our share of copromotion profits. F. Hoffmann-La Roche Ltd. sells rituximab outside the U.S., except in Japan where it copromotes RITUXAN in collaboration with Zenyaku Kogyo Co. Ltd. We received royalties on sales of rituximab outside of the U.S. of $67.9 million in 2003 as compared to $45.4 million in 2002. RITUXAN is the trade name used for rituximab in the U.S., Canada and Japan, and MabThera is the trade name in the European Union, or EU. In this Form 10-K, we refer to rituximab, RITUXAN and MabThera collectively as RITUXAN, except where we have otherwise indicated. In February 2002, ZEVALIN became the first radioimmunotherapy approved by the FDA for the treatment of cancer. ZEVALIN is approved as a treatment for relapsed or refractory low-grade, follicular, or transformed B-cell NHL including patients with RITUXAN refractory follicular NHL. We launched ZEVALIN in the U.S. in April 2002. In 2003, sales of ZEVALIN in the U.S. generated revenues of $19.6 million as compared to revenues of $13.7 million in 2002. Outside the U.S., we have licensed our marketing rights in ZEVALIN to Schering AG. In January 2004, the European Agency for the Evaluation of Medicinal Products, or EMEA, the regulatory authority in the EU, granted marketing approval of ZEVALIN in the EU for the treatment of adult patients with CD20+ follicular B-cell NHL who are refractory to or have relapsed following RITUXAN therapy. AMEVIVE was approved in the U.S. in January 2003 for the treatment of adult patients with moderate-to-severe chronic plaque psoriasis who are candidates for systemic therapy or phototherapy. In 2003, sales of AMEVIVE generated revenues of $40.4 million. In February 2003, the European Committee for Proprietary Medicinal Products, the scientific advisory board of the EMEA, determined that more information was required to approve AMEVIVE in the EU.