<PAGE>   1

                                  FORM 10-K/A

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549
      (Mark One)

          [X]  ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
                SECURITIES EXCHANGE ACT OF 1934 [FEE REQUIRED]
                 For the fiscal year ended December 31, 1996

                                       OR

          [ ]  TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
                 SECURITIES EXCHANGE ACT OF 1934 [NO FEE REQUIRED]

                        Commission file number: 0-12042


                                  BIOGEN, INC.
             (Exact name of Registrant as specified in its charter)


          Massachusetts                            04-3002117
     (State or other jurisdiction               (I.R.S. Employer
   of incorporation or organization)           Identification No.)


              14 Cambridge Center, Cambridge, Massachusetts 02142
               (Address of principal executive offices)(zip code)

       Registrant's telephone number, including area code: (617) 679-2000


        Securities registered pursuant to Section 12(b) of the Act: None


      Securities registered pursuant to Section 12(g) of the Act:   

                         Common Stock, $.01 par value
                               (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  X   No
                  -----   -----

     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 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. [ ]

     Aggregate market value of Common Stock held by nonaffiliates of the
Registrant at February 13, 1997: $3,526,097,099 (excludes shares held by
directors).  Exclusion of shares held by any person should not be construed to
indicate that such person possesses the power, direct or indirect, to direct or
cause the direction of management or policies of the Registrant, or that such
person is controlled by or under common control with the Registrant.  Common
Stock outstanding at February 13, 1997: 73,060,328 shares.

                      DOCUMENTS INCORPORATED BY REFERENCE

     Portions of the Registrant's definitive Proxy Statement for its 1997
Annual Meeting of Stockholders are incorporated by reference into Part III of
this Report, and portions of the Registrant's 1996 Annual Report to
Shareholders are incorporated by reference into Parts II and IV of this Report.
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(3) Exhibits

EXHIBIT NO.      DESCRIPTION
-----------      -----------
(3.1)            Articles of Organization, as amended

(3.2)            By-Laws, as amended (k)

(4.1)            Form of Common Stock Share Certificate (m)

(4.2)            Certificate of Designation of Series A Junior Participating
                 Preferred Stock (f)

(4.3)            Rights Agreement dated as of May 8, 1989 between Registrant
                 and The First National Bank of Boston, as Rights Agent (f)

(10.1)           Independent Consulting and Project Agreement dated as of June
                 29, 1979 between Registrant and Kenneth Murray (a)**

(10.2)           Letter Agreement dated September 23, 1995 with Sir Kenneth
                 Murray relating to renewal of Independent Consulting
                 Agreement (r)**

(10.3)           Minute of Agreement dated February 5, 1981 among Registrant,
                 The University Court of the University of Edinburgh and
                 Kenneth Murray (a)**

(10.4)           Independent Consulting Agreement dated as of June 29, 1979
                 between Registrant and Phillip A. Sharp (a)**

(10.5)           Letter Agreement dated December 15, 1995 with Phillip Sharp
                 relating to chairmanship of Scientific Board and renewal of
                 Independent Consulting Agreement (r)**

(10.6)           Project Agreement dated as of December 14, 1979 between
                 Registrant and Phillip A. Sharp (a)**

(10.7)           Share Restriction and Repurchase Agreement dated as of
                 December 15, 1979 between Registrant and Phillip A.
                 Sharp (a)**

(10.8)           Consulting Agreement dated as of April 1, 1991, as amended,
                 between Registrant and Alexander G. Bearn (i)**

(10.9)           Letter Agreement dated April 14, 1995 with Dr. Alexander
                 Bearn relating to renewal of Independent Consulting
                 Agreement (r)**

(10.10)          Form of Amendment dated July 1, 1988 to Independent
                 Consulting Agreement between Registrant and Scientific Board
                 Members (e)**

(10.11)          Form of Share Purchase Agreement between Registrant and
                 Scientific Board Members (a)**

(10.12)          Form of Stock Option Agreement between Registrant and
                 certain outside directors (c)**
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(10.13)          Letter regarding employment of James L. Vincent dated
                 September 23, 1985 (b)**

(10.14)          Form of Stock Option Agreement with James L. Vincent
                 under 1985 Non-Qualified Stock Option Plan (k)**

(10.15)          Form of Stock Option Agreement with James L. Vincent
                 under 1985 Non-Qualified Stock Option Plan (1995) (r)**

(10.16)          Letter dated December 13, 1989 regarding employment of
                 Dr. Irving H. Fox (h)**

(10.17)          Letter dated April 7, 1993 regarding employment of Dr.
                 Joseph M. Davie (l)**

(10.18)          Letter dated January 12, 1994 regarding employment of James
                 R. Tobin (n)**

(10.19)          Form of Indemnification Agreement between Registrant and
                 each Director and Executive Officer (e)**

(10.20)          Second Amended and Restated Agreement and Certificate of
                 Limited Partnership dated as of May 15, 1984 among Biogen
                 Medical Products, Inc. as General Partner and certain
                 limited partners (g)

(10.21)          First Amendment dated December 22, 1986 to Agreement and
                 Certificate of Limited Partnership (c)

(10.22)          Technology License Agreement dated May 15, 1984 between
                 Biogen B.V. and Biogen Medical Products Limited Partnership
                 (g)

(10.23)          Development Contract dated May 15, 1984 between Biogen
                 B.V. and Biogen Medical Products Limited Partnership (g)

(10.24)          Amendment dated December 22, 1986 to Development Contract (c)

(10.25)          Amendment dated January 1, 1987 to Development Contract (d)

(10.26)          Joint Venture Option Agreement dated May 15, 1984 between
                 Biogen, Inc. and Biogen Medical Products Limited Partnership
                 (g)

(10.27)          Purchase Option Agreement dated May 15, 1984 between
                 Biogen B.V. and the limited partners of Biogen Medical
                 Products Limited Partnership (g)

(10.28)          Guaranty dated May 15, 1984 to Biogen Medical Products
                 Limited Partnership by Registrant guaranteeing certain
                 obligations of Biogen Medical Products, Inc., Biogen B.V.
                 and Biogen, Inc. to the Partnership (g)

(10.29)          Demand Loan Agreement dated October 1, 1989 between Biogen
                 Medical Products Limited Partnership and Biogen Medical
                 Products, Inc. (g)

(10.30)          Certificate of Cancellation of Certificate of Limited
                 Partnership of Biogen Medical Products Limited Partnership
                 dated December 24, 1996
<PAGE>   4

(10.31)          Standard Form Commercial Lease dated January 29, 1981
                 between Ira C. Foss and Ira C. Foss, Jr., as Trustees of
                 Eastern Realty Trust, and B. Leasing, Inc. (g)

(10.32)          Letter of May 24, 1989 exercising option under Standard
                 Form Commercial Lease dated January 29, 1981 (g)

(10.33)          Lease Extension Agreement dated February 20, 1990 between
                 Eastern Realty Trust and Registrant (g)

(10.34)          Standard Form Commercial Lease dated June 1, 1989 between
                 Eastern Realty Trust and Registrant (g)

(10.35)          Cambridge Center Lease dated October 4, 1982 between
                 Mortimer Zuckerman, Edward H. Linde and David Barrett, as
                 Trustees of Fourteen Cambridge Center Trust, and B. Leasing,
                 Inc. (a)

(10.36)          First Amendment to Lease dated January 19, 1989 amending
                 Cambridge Center Lease dated October 4, 1982 (k)

(10.37)          Second Amendment to Lease dated March 8, 1990 amending
                 Cambridge Center Lease dated October 4, 1982 (k)

(10.38)          Third Amendment to Lease dated September 25, 1991 amending
                 Cambridge Center Lease dated October 4, 1982 (k)

(10.39)          Lease dated October 6, 1993 between North Parcel Limited
                 Partnership and Biogen Realty Limited Partnership (n)

(10.40)          1983 Employee Stock Purchase Plan, as amended and restated
                 through September 22, 1995 (r)**

(10.41)          1982 Incentive Stock Option Plan as amended through April 25,
                 1995 and restated with form of Option Agreement (q)**

(10.42)          1985 Non-Qualified Stock Option Plan as amended through
                 April 25, 1995 and restated with form of Option Agreement
                 (q) **

(10.43)          1987 Scientific Board Stock Option Plan as amended through
                 April 3, 1992 and restated with form of Option Agreement (j)**

(10.44)          Voluntary Executive Supplemental Savings Plan (p)**

(10.45)          Supplemental Executive Retirement Plan (p)**

(10.46)          Voluntary Board of Directors Savings Plan (p)**

(10.47)          Exclusive License and Development Agreement dated December
                 8, 1979 between Registrant and Schering Corporation (a)

(10.48)          Amendatory Agreement dated May 14, 1985 to Exclusive
                 License and Development
<PAGE>   5
                 Agreement dated December 8, 1979 (b)

(10.49)          Amendment and Settlement Agreement dated September 29,
                 1988 to Exclusive License and Development Agreement dated
                 December 8, 1979 (k)

(10.50)          Amendment dated March 20, 1989 to Exclusive License and
                 Development Agreement dated December 8, 1979 (k)

(10.51)          License Agreement (United States) dated March 28, 1988
                 between Registrant and SmithKline Beecham Biologicals, s.a.
                 (as successor to Smith Kline-R.I.T, s.a.) (k)

(10.52)          License Agreement (International) dated March 28, 1988
                 between Registrant and SmithKline Beecham Biologicals, s.a.
                 (as successor to Smith Kline-R.I.T., s.a.) (k)

(10.53)          Sublicense Agreement dated as of February 15, 1990 among
                 Registrant, SmithKline Beecham Biologicals, s.a (as successor
                 to SmithKline Biologicals, s.a.) and Merck and Co., Inc. (k)

(10.54)          Supplemental Amendment and Agreement dated as of March 1,
                 1994 between the Registrant and Schering Corporation (o)

(10.55)          Letter agreement amending employment arrangement between
                 the Registrant and James L. Vincent dated as of November 21,
                 1996 *  **

(11)             Computation of Earnings per Share

(12)             None

(13)             Incorporated portions from Biogen, Inc. 1996 Annual Report
                 to Shareholders

(21)             Subsidiaries of the Registrant

(24.1)           Consent of Price Waterhouse LLP (Included in Part IV hereof)

(29)             None

            (a)  Previously filed with the Commission as an exhibit to
                 Registration Statement on Form S-1, File No. 2-81689 and
                 incorporated herein by reference.

            (b)  Previously filed with the Commission as an exhibit to
                 Registrant's Annual Report on Form 10-K for the year ended
                 December 31, 1985, as amended, File No. 0-12042 and
                 incorporated herein by reference.

            (c)  Previously filed with the Commission as an exhibit to
                 Registrant's Annual Report on Form 10-K for the year ended
                 December 31, 1986, as amended, File No. 0-12042 and
                 incorporated herein by reference.

            (d)  Previously filed with the Commission as an exhibit to
                 Registrant's Annual Report on Form 10-K for the year ended
                 December 31, 1987, File No. 0-12042 and incorporated herein
                 by reference.
<PAGE>   6

            (e)  Previously filed with the Commission as an exhibit to
                 Registrant's Annual Report on Form 10-K for the year ended
                 December 31, 1988, File No. 0-12042 and incorporated herein
                 by reference.

            (f)  Previously filed with the Commission as an exhibit to
                 Registration Statement on Form 8-A, File No. 0-12042, filed
                 May 26, 1989 and incorporated herein by reference.

            (g)  Previously filed with the Commission as an exhibit to
                 Registrant's Annual Report on Form 10-K for the year ended
                 December 31, 1989, File No. 0-12042, and incorporated herein
                 by reference.

            (h)  Previously filed with the Commission as an exhibit to
                 Registrant's Annual Report on Form 10-K for the year ended
                 December 31, 1990, File No. 0-12042, and incorporated herein
                 by reference.

            (i)  Previously filed with the Commission as an exhibit to
                 Registrant's Annual Report on Form 10-K for the year ended
                 December 31, 1991, File No. 0-12042, and incorporated herein
                 by reference.

            (j)  Previously filed with the Commission as an exhibit to
                 Registrant's Quarterly Report on Form 10-Q for the quarter
                 ended June 30, 1992, File No. 0-12042, and incorporated
                 herein by reference.

            (k)  Previously filed with the Commission as an exhibit to the
                 Registrant's Annual Report on Form 10-K for the fiscal year
                 ended December 31, 1993, File No. 0-12042, and incorporated
                 herein by reference.

            (l)  Previously filed with the Commission as an exhibit to the
                 Registrant's Quarterly Report on Form 10-Q for the quarter
                 ended June 30, 1993, File No. 0-12042, and incorporated
                 herein by reference.

            (m)  Previously filed with the Commission as an exhibit to
                 Registration Statement on Form S-3, File No. 33-51639, and
                 incorporated herein by reference.

            (n)  Previously filed with the Commission as an exhibit to
                 Registrant's Annual Report on Form 10-K for the year ended
                 December 31, 1994, File No. 0-12042, and incorporated herein
                 by reference.

            (o)  Previously filed with the Commission as an exhibit to the
                 Registrant's Quarterly Report on Form 10-Q for the quarter
                 ended March 31, 1994, File No. 0-12042, and incorporated
                 herein by reference.

            (p)  Previously filed with the Commission as an exhibit to the
                 Registrant's Annual Report on Form 10-K for the fiscal year
                 ended December 31, 1994, File No. 0-12042, and incorporated
                 herein by reference.

            (q)  Previously filed with the Commission as an exhibit to the
                 Registrant's Quarterly Report on Form 10-Q for the quarter
                 ended June 30, 1995, File No. 0-12042, and incorporated
                 herein by reference.

            (r)  Previously filed with the Commission as an exhibit to the
                 Registrant's Annual Report on
<PAGE>   7

                 Form 10-K for the fiscal year ended December 31, 1995, File 
                 No. 0-12042, and in incorporated herein by reference.

     * Filed herewith
    ** Management contract or compensatory plan or arrangement
<PAGE>   8

    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.

BIOGEN, INC.

By: /s/ James R. Tobin
    -------------------------------------
    President and Chief Executive Officer

Dated  March 27, 1997
<PAGE>   9

                                 EXHIBIT INDEX
                                 -------------


EXHIBIT NO.      DESCRIPTION
-----------      -----------

(10.55)          Letter agreement amending employment arrangement between
                 the Registrant and James L. Vincent dated as of 
                 November 21, 1996