<PAGE>   1
                       SECURITIES AND EXCHANGE COMMISSION     TOTAL PAGES -   21
                             WASHINGTON, D.C. 20549           EXHIBIT INDEX - 21
                   -------------------------------------------

                                    FORM 10-Q

(MARK ONE)

[X]  Quarterly Report Pursuant to Section 13 or 15 (d) of the Securities
Exchange Act of 1934.

For the quarterly period ended  September 30, 1999
                              --------------------------------------------------

                                       OR

[ ]  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 0-12042

                   -------------------------------------------

                                   BIOGEN,INC.

             ------------------------------------------------------

             (Exact name of registrant as specified in its charter)

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

 14 Cambridge Center, Cambridge, MA                       02142
----------------------------------------    ------------------------------------
(Address of principal executive offices)                (Zip Code)


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

Former name, former address and former fiscal year, if changed since last
report: Not Applicable.

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
                             --------      --------

Number of shares outstanding of each of the issuer's classes of common stock, as
of October 29, 1999:

Common Stock, par value $0.01                           150,241,606
-----------------------------                         ----------------
   (Title of each class)                              Number of Shares


<PAGE>   2


                                                                          Page 2

                                  BIOGEN, INC.

                                      INDEX

<TABLE>
<CAPTION>
PART I - FINANCIAL INFORMATION                                                                                 Page No.

<S>                                                                                                                <C>
Condensed Consolidated Statements of Income -
      Three and nine months ended September 30, 1999 and 1998                                                      3

Condensed Consolidated Balance Sheets -
      September 30, 1999 and December 31, 1998                                                                     4

Condensed Consolidated Statements of Cash Flows -
      Nine months ended September 30, 1999 and 1998                                                                5

Notes to Condensed Consolidated Financial Statements                                                               6

Management's Discussion and Analysis of Financial
      Condition and Results of Operations                                                                         12

PART II - OTHER INFORMATION                                                                                       20
</TABLE>








Note concerning trademarks:           AVONEX(R) is a registered trademark of
                                      Biogen, Inc.


<PAGE>   3


                                                                          Page 3

                          BIOGEN, INC. AND SUBSIDIARIES
                   CONDENSED CONSOLIDATED STATEMENTS OF INCOME
                                   (unaudited)
                    (in thousands, except per share amounts)


<TABLE>
<CAPTION>
                                                 Three Months Ended               Nine Months Ended
                                                    September 30,                   September 30,
                                                1999            1998            1999            1998
                                                ----            ----            ----            ----

<S>                                           <C>             <C>             <C>             <C>
REVENUES:

 Product sales                                $163,448        $107,492        $440,620        $270,665
 Royalties                                      44,983          38,412         128,460         118,523
                                              --------        --------        --------        --------

   Total revenues                              208,431         145,904         569,080         389,188
                                              --------        --------        --------        --------

COSTS and EXPENSES:

   Cost of sales                                28,498          19,513          80,329          51,557
   Research and development                     58,958          49,083         160,886         128,338
   Selling, general and administrative          36,484          27,011         107,344          81,495
                                              --------        --------        --------        --------

Total costs and expenses                       123,940          95,607         348,559         261,390
                                              --------        --------        --------        --------

Income from operations                          84,491          50,297         220,521         127,798
Other income, net                                8,092           5,685           5,006          18,846
                                              --------        --------        --------        --------
INCOME BEFORE INCOME TAXES                      92,583          55,982         225,527         146,644
Income taxes                                    30,554          18,417          74,426          49,859
                                              --------        --------        --------        --------

NET INCOME                                    $ 62,029        $ 37,565        $151,101        $ 96,785
                                              ========        ========        ========        ========

BASIC EARNINGS PER SHARE                      $   0.41        $   0.25        $   1.01        $   0.66
                                              ========        ========        ========        ========
DILUTED EARNINGS PER SHARE                    $   0.39        $   0.24        $   0.96        $   0.63
                                              ========        ========        ========        ========

SHARES USED IN CALCULATING:
Basic earnings per share                       150,108         147,564         149,851         147,659
                                              ========        ========        ========        ========
Diluted earnings per share                     158,198         154,516         157,768         153,917
                                              ========        ========        ========        ========
</TABLE>


See Notes to Condensed Consolidated Financial Statements.


<PAGE>   4


                                                                          Page 4

                          BIOGEN, INC. AND SUBSIDIARIES
                      CONDENSED CONSOLIDATED BALANCE SHEETS
                                 (in thousands)


<TABLE>
<CAPTION>
                                                    September 30, 1999      December 31, 1998
                                                          1999                    1998
                                                    ------------------      -----------------
                                                       (unaudited)

<S>                                                    <C>                     <C>
ASSETS
   Current assets
     Cash and cash equivalents                         $    73,494             $    25,445
     Marketable securities                                 599,146                 491,469
     Accounts receivable, net                              129,863                 101,281
     Deferred tax asset                                     24,873                  26,584
     Other current assets                                   52,130                  49,365
                                                       -----------             -----------
     Total current assets                                  879,506                 694,144
                                                       -----------             -----------

   Property, plant and equipment

     Cost                                                  312,883                 269,038
     Less accumulated depreciation                         104,440                  86,487
                                                       -----------             -----------

     Property, plant and equipment, net                    208,443                 182,551
                                                       -----------             -----------

Patents, net                                                14,186                  15,869
Marketable securities                                       22,638                  12,668
Other assets                                                15,227                  19,483
                                                       -----------             -----------

                                                       $ 1,140,000             $   924,715
                                                       ===========             ===========

LIABILITIES AND SHAREHOLDERS' EQUITY
   Current liabilities
     Accounts payable                                  $    19,975             $    24,896
     Current portion of long-term debt                       4,888                   4,888
     Accrued expenses and other                            103,389                 105,305
                                                       -----------             -----------
     Total current liabilities                             128,252                 135,089
                                                       -----------             -----------

   Long-term debt, less current portion                     53,711                  56,960
   Other long-term liabilities                              15,540                  14,053
   Commitments and contigencies                                 --                      --

   Shareholders' equity
     Common stock                                            1,507                     741
     Additional paid-in capital                            663,265                 538,847
     Retained earnings                                     304,759                 213,507
     Accumulated other comprehensive income                  5,537                 (13,165)
     Treasury stock, at cost                               (32,571)                (21,317)
                                                       -----------             -----------

   Total shareholders' equity                              942,497                 718,613
                                                       -----------             -----------

                                                       $ 1,140,000             $   924,715
                                                       ===========             ===========
</TABLE>


See Notes to Condensed Consolidated Financial Statements.


<PAGE>   5


                                                                          Page 5

                          BIOGEN, INC. AND SUBSIDIARIES
                 CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS
                                   (unaudited)
                                 (in thousands)

<TABLE>
<CAPTION>
                                                                        Nine Months Ended
                                                                          September 30,
                                                                   --------------------------
                                                                   1999                  1998
                                                                   ----                  ----
<S>                                                             <C>                   <C>
CASH FLOWS FROM OPERATING ACTIVITIES
   Net income                                                   $ 151,101             $  96,785
   Adjustments to reconcile net income
     to net cash provided from
     operating activities:
     Depreciation and amortization                                 22,563                17,980
     Deferred income taxes                                          1,711                11,484
     Write-down of non-current marketable securities               15,287                    --
     Other                                                          1,610                   552
     Changes in:
       Accounts receivable                                        (28,582)               (3,373)
       Other current and other assets                               1,116               (12,469)
       Accounts payable, accrued expenses
         and other current and long term
         liabilities                                               (1,969)               14,869
                                                                ---------             ---------
   Net cash provided from operating activities                    162,837               125,828
                                                                ---------             ---------
CASH FLOWS FROM INVESTING ACTIVITIES
   Purchases of marketable securities                            (468,988)             (398,668)
   Proceeds from sales and maturities of
     marketable securities                                        356,681               357,925
   Investment in collaborative partners                                --                (5,000)
   Acquisitions of property and equipment                         (43,845)              (19,473)
   Additions to patents                                            (2,927)               (3,854)
                                                                ---------             ---------
     Net cash used by investing activities                       (159,079)              (69,070)
                                                                ---------             ---------

CASH FLOWS FROM FINANCING ACTIVITIES
   Repayments of note payable                                          --                (6,065)
   Payments of long-term debt                                      (3,249)               (3,250)
   Purchases of treasury stock                                   (106,453)              (50,850)
   Proceeds from put warrants                                      19,947                    --
   Issuance of common stock, stock option
     exercises and related tax benefits                           134,046                27,207
                                                                ---------             ---------
     Net cash from financing activities                            44,291               (32,958)
                                                                ---------             ---------

NET INCREASE IN CASH AND
     CASH EQUIVALENTS                                              48,049                23,800

CASH AND CASH EQUIVALENTS,
     BEGINNING OF PERIOD                                           25,445                70,358
                                                                ---------             ---------

CASH AND CASH EQUIVALENTS,
     END OF PERIOD                                              $  73,494             $  94,158
                                                                =========             =========
</TABLE>
See Notes to Condensed Consolidated Financial Statements.


<PAGE>   6


                                                                          Page 6

                          BIOGEN, INC. AND SUBSIDIARIES
              NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS
                                   (unaudited)






1.   In the opinion of management, the accompanying unaudited condensed
     consolidated financial statements include all adjustments, consisting of
     only normal recurring accruals, necessary to present fairly the financial
     position, results of operations and cash flows of Biogen, Inc. and its
     subsidiaries (the "Company"). The Company's accounting policies are
     described in the Notes to Consolidated Financial Statements in the
     Company's 1998 Annual Report on Form 10-K. Interim results are not
     necessarily indicative of the operating results for the full year.

     The preparation of financial statements in conformity with generally
     accepted accounting principles requires management to make estimates and
     assumptions that affect the reported amounts of assets and liabilities
     and disclosure of contingent assets and liabilities at the date of the
     financial statements, and the reported amounts of revenues and expenses
     during the reporting period. Actual results could differ from those
     estimates. Certain amounts for the nine months ended September 30, 1998
     have been reclassified to conform to the current period presentation.

     The carrying amounts reflected in the consolidated balance sheet for cash
     and cash equivalents, accounts receivable, other current assets, accounts
     payable, and accrued expense and other, approximate fair value due to the
     short term maturities of these instruments. Marketable securities are
     carried at fair value based on quoted market prices, consistent with the
     requirements of Statement of Financial Accounting Standards No. 115,
     "Accounting for Certain Investments in Debt and Equity Securities". The
     Company's long term debt approximates fair value based on dealer quotes.

     Inventories, which are included in other current assets, are stated at the
     lower of cost or market with cost determined under the first-in/first-out
     ("FIFO") method. Raw materials include inventory used in the production of
     pre-clinical and clinical products, which are expensed as research and
     development costs when consumed. Inventories are as follows:

<TABLE>
<CAPTION>
                                 (In thousands)
                         --------------------------------
                         September 30,       December 31,
                             1999               1998
                         -------------       ------------

<S>                        <C>                <C>
Raw materials              $ 5,731            $ 4,878
Work in process             12,361             17,585
Finished goods              17,354             13,402
                           -------            -------
                           $35,446            $35,865
                           =======            =======
</TABLE>




     Property and equipment is carried at cost and depreciation is calculated on
     the straight-line basis over the estimated useful lives of the assets.
     Leasehold improvements are amortized over the lesser of the useful life or
     the term of the respective lease. Maintenance of computer systems,
     including maintenance to make software Year 2000 compliant, is expensed as
     incurred. The Company capitalizes certain incremental costs associated with
     the


<PAGE>   7


                                                                          Page 7

     validation effort required for licensing by the FDA of a manufacturing
     facility for the production of a commercially approved drug. These costs
     include direct labor and certain material costs directly related to the
     validation effort. Buildings and equipment are depreciated over the
     estimated useful lives ranging from 30 to 40 and 3 to 10 years,
     respectively. The carrying value of property and equipment is subject to
     review for impairment whenever events or changes in circumstances indicate
     that the carrying amount of the asset may not be recoverable. Impairments
     are recognized when the expected future operating cash flows derived from
     the property and equipment are less than their carrying value.

     The Company has foreign currency forward contracts to hedge specific
     forecasted transactions denominated in foreign currencies. All foreign
     currency forward contracts have durations of ninety days to 21 months.
     These contracts are designated as cash flow hedges and accordingly, when
     effective, any unrealized gains or losses on these contracts are reported
     in other comprehensive income. Realized gains and losses for the effective
     portion are recognized with the underlying hedge transaction. The notional
     settlement amount of the forwards outstanding at September 30, 1999 was
     approximately $226.4 million. These contracts had a fair value of
     approximately $376,000 representing an unrealized loss and were included in
     accrued expenses and other at September 30, 1999 compared to a $3,000
     unrealized gain at December 31, 1998.

     The Company did not recognize in earnings a gain or loss for the period
     ended September 30, 1999 relating to any amount of hedge ineffectiveness
     nor was any amount excluded from the assessment of hedge effectiveness. The
     Company recognized a $1.7 million gain in product revenue and a $429,000
     gain in royalty revenue for the settlement of certain effective cash flow
     hedge instruments for the three-month period ended September 30, 1999. The
     Company recognized a $4.5 million gain in product revenue and a $1.7
     million gain in royalty revenue for the settlement of certain effective
     cash flow hedge instruments for the nine-month period ended September 30,
     1999. These settlements were recorded in the same period as the related
     forecasted transactions affecting earnings.

     Revenues from product sales are recognized when product is shipped and are
     net of applicable allowances for returns, rebates and other applicable
     discounts and allowances. The Company prepares its estimates for sales
     returns and allowances, discounts and rebates quarterly based primarily on
     historical experience updated for changes in facts and circumstances, as
     appropriate.


     The Company receives royalty revenues under license agreements with a
     number of third parties that sell products based on technology developed by
     the Company or to which the Company has rights. The license agreements
     provide for the payment of royalties to the Company based on sales of the
     licensed product. The Company records these revenues based on estimates of
     the sales that occurred during the relevant period. The relevant period
     estimates of sales are based on interim data provided by licensees and
     analysis of historical royalties paid to the Company (adjusted for any
     changes in facts and circumstances, as appropriate). The Company maintains
     regular communication with its licensees in order to gauge the
     reasonableness of its estimates. Differences between actual royalty
     revenues and estimated royalty revenues are reconciled and adjusted for in
     the following quarter. Historically, adjustments have not been material
     based on actual amounts paid by licensees. Many of the license agreements
     also provide for the payment of one-time, non-refundable fees when the
     agreement is signed or when commercial goals are achieved. These fees are
     recorded as revenue in accordance with the terms of the particular
     agreement. There are no future performance obligations on the part of the
     Company under these license agreements.


<PAGE>   8


                                                                          Page 8


2.   As of September 30, 1999, the Company had $18 million outstanding under a
     floating rate term loan secured by a laboratory and office building in
     Cambridge, Massachusetts. Principal payments of $1.7 million per annum are
     due through 2004 with the balance due on May 8, 2005. The Company also
     entered into an interest rate swap agreement, with the same bank, fixing
     its interest rate at 7.5% during the remaining term of the loan, payable
     semi-annually.

     As of September 30, 1999, the Company had $40 million outstanding under a
     floating rate loan agreement with a bank for financing the construction of
     the Company's biological manufacturing facility in North Carolina (the
     "Construction Loan"). The Company completed construction of its biological
     manufacturing facility in 1997. The Construction Loan is secured by the
     facility. Payments of $805,000 are due quarterly through 2006 with the
     balance due on March 31, 2007. The Company also entered into an interest
     rate swap agreement, with the same bank, fixing its interest rate at 7.75%
     during the remaining term of the loan, payable quarterly.

     Terms of the loan agreements include various covenants, including financial
     covenants, which require the Company to maintain minimum net worth, cash
     flow and various financial ratios.

     The Company uses interest rate swap agreements to mitigate the risk
     associated with its floating rate debt and recognizes the differential as
     interest expense. The interest rate swap agreements have been designated as
     cash flow hedges. The Company did not recognize in earnings a gain or loss
     during the reporting period relating to any amount of hedge ineffectiveness
     nor was any amount excluded from the assessment of hedge effectiveness. The
     fair values of the swap agreements at September 30, 1999, representing the
     cash requirements of the Company to settle the agreements, were
     approximately $750,000 representing an unrealized loss and were included in
     accrued expenses and other at September 30, 1999 compared to a $4.1 million
     unrealized loss at December 31, 1998.

3.   Other income, net consists of the following (in thousands):

<TABLE>
<CAPTION>
                                        Three Months Ended                         Nine Months Ended
                                           September 30,                             September 30,
                                     -------------------------                --------------------------
                                     1999                 1998                 1999                 1998
                                     ----                 ----                -----                 ----
<S>                                <C>                  <C>                  <C>                  <C>
Interest income                    $  9,450             $  7,033             $ 25,713             $ 20,964
Interest expense                     (1,171)              (1,472)              (3,527)              (4,709)
Other income/(expense)                 (187)                 124              (17,180)               2,591
                                   --------             --------             --------             --------

Total other income, net            $  8,092             $  5,685             $  5,006             $ 18,846
                                   ========             ========             ========             ========
</TABLE>


     The decrease in other income, net for the nine months ended
<PAGE>   9


                                                                          Page 9

     September 30, 1999 compared to the same period in 1998 was primarily
     attributable to a $15 million write-down of certain non-current marketable
     securities, partially offset by the increase in interest income.

     As part of its strategic product development efforts, the Company invests
     in equity securities of certain biotechnology companies with which it has
     collaborative agreements. In December of 1996, Biogen purchased
     approximately 1.5 million shares of Creative BioMolecules, Inc. common
     stock for $18 million. In March of 1997, Biogen purchased approximately
     670,000 shares of CV Therapeutics, Inc. common stock for $7 million. In
     March of 1998, the Company purchased approximately 435,000 shares of
     CuraGen common stock for $5 million and converted 100,000 shares of CuraGen
     Series E Preferred Stock valued at $1 million to CuraGen common stock. Each
     of these small emerging companies is principally engaged in researching,
     developing or manufacturing drugs for human health care. In recent periods,
     the value of these publicly-traded marketable securities had been
     negatively impacted by general market conditions for small cap
     biotechnology stocks.

     As a matter of policy, Biogen determines on a quarterly basis whether a
     decline in the fair value of a marketable security is other than temporary.
     Unrealized gains and losses on marketable securities are included in other
     comprehensive income in shareholders' equity, net of related tax effects.
     If a decline in the fair value of a marketable security below the Company's
     cost basis is determined to be other than temporary, such marketable
     security is written down to its estimated fair value with a charge to
     current earnings.

     Up through and including the assessment at June 30, 1999, the Company
     concluded that substantial evidence existed suggesting that the value of
     the investments described above would recover to at least the Company's
     purchase price. Such evidence included the prospects for favorable clinical
     trial results, new product initiatives, and new collaborative agreements.
     However, given the lack of any substantial price recovery during the
     quarter ended June 30, 1999, and the amount of time elapsed since the
     decline in value began, the Company concluded that it had become unclear
     over what period such price recovery would take place. As a result, it was
     determined that the positive evidence suggesting that the investments would
     recover to at least the Company's purchase price was not sufficient to
     overcome the presumption that the current market price of the investments
     was the best indicator of value at June 30, 1999. Accordingly, the related
     unrealized losses of $15 million were recognized as other expense.

4.   Income tax expense as a percentage of pre-tax income for the quarters ended
     September 30, 1999 and 1998 was 33%, respectively. Income tax expense as a
     percentage of pre-tax income for the nine months ended September 30, 1999
     and 1998 was 33% and 34%, respectively. The effective tax rate varied from
     U.S. statutory rates in the three and nine-month periods of 1999 and 1998,
     primarily due to increased European sales and to the utilization of
     research and development credits.

5.   Dilutive stock options include outstanding options under the Company's
     stock option plans. Options to purchase 54,000 shares of common stock were
     outstanding at September 30, 1999 but not included in the computation of


<PAGE>   10


                                                                         Page 10

     diluted earnings per share because the options' exercise prices were
     greater than the average market price during the period. Below is a summary
     of the shares used in calculating basic and diluted earnings per share (in
     thousands):

<TABLE>
<CAPTION>
                                                 Three Months Ended                     Nine Months Ended
                                                    September 30,                         September 30,
                                              --------------------------            --------------------------
                                               1999               1998               1999               1998
                                              -------            -------            -------            -------
<S>                                           <C>                <C>                <C>                <C>
Weighted average number of shares
 of common stock outstanding                  150,108            147,564            149,851            147,659
Dilutive stock options                          8,090              6,952              7,917              6,258
                                              -------            -------            -------            -------

Shares used in calculating diluted
 earnings per share                           158,198            154,516            157,768            153,917
                                              =======            =======            =======            =======
</TABLE>

     On June 11, 1999, the Board of Directors declared a two-for-one stock split
     to be effected in the form of a stock dividend of one share of common stock
     for each share outstanding. The stock dividend was paid on June 25, 1999 to
     shareholders of record at the close of business on June 11, 1999. All
     references to the number of shares and per share amounts in the financial
     statements have been restated to reflect the effect of the stock split.

     On February 22, 1999, the Company announced that its Board of Directors had
     authorized the repurchase of up to 8 million shares of the Company's common
     stock. The repurchased stock will provide the Company with treasury shares
     for general corporate purposes, such as stock to be issued under employee
     stock option and stock purchase plans. Stock purchases are expected to
     occur from time to time through 2000. The stock repurchase program may be
     discontinued at any time. To enhance the stock repurchase program, the
     Company sold put warrants to and purchased call options from independent
     third parties covering a large portion of the shares intended to be
     repurchased. The outstanding put warrants permit a net-share settlement at
     the Company's option. The put warrants sold in connection with the
     Company's stock repurchase program may have an additional dilutive effect.

6.   Comprehensive income is comprised of net income and other comprehensive
     income. Other comprehensive income includes certain changes in equity that
     are excluded from net income, such as, translation adjustments, and
     unrealized holding gains and losses on available-for-sale marketable
     securities and certain derivative instruments. Comprehensive income for the
     three months ended September 30, 1999 and 1998 was $63 million and $38
     million, respectively. Comprehensive income for the nine months ended
     September 30, 1999 and 1998 was $170 million and $92 million, respectively.

7.   On July 3, 1996, Berlex Laboratories, Inc. ("Berlex") filed suit against
     Biogen in the United States District Court for the District of New Jersey
     alleging infringement by Biogen of Berlex's "McCormick" patent in the
     United States in the production of Biogen's AVONEX(R) (Interferon beta-la).
     In November 1996, Berlex's New Jersey action was transferred to the U.S.
     District Court in Massachusetts and consolidated for pre-trial purposes
     with a related declaratory judgement action previously filed by Biogen. On
     August 18, 1998, Berlex filed a second suit against Biogen alleging
     infringement by Biogen of a patent which was issued to Berlex in August
     1998 and which is


<PAGE>   11


                                                                         Page 11

     related to the McCormick patent. On September 23, 1998, the cases were
     consolidated for pre-trial and trial purposes. Berlex seeks a judgement
     granting it damages, a trebling of any damages awarded and a permanent
     injunction restraining Biogen from the alleged infringement. An unfavorable
     ruling in the Berlex suit could have a material adverse effect on the
     Company's results of operations and financial position. The Company
     believes that it has meritorious defenses to the Berlex claims, but the
     ultimate outcome is not currently determinable. As a result, an estimate of
     any potential loss or range of loss cannot be made at this time. A full
     hearing on the parties' summary judgement motions originally scheduled for
     November 1999 has been postponed. A trial is tentatively scheduled for
     February 2000 but may also be postponed.

     On October 14, 1998, the Company filed an opposition with the Opposition
     Division of the European Patent Office to oppose a European patent (the
     "Rentschler patent") issued to Dr. Rentschler Biotechnologie GmbH
     ("Rentschler") with certain claims regarding compositions of matter of beta
     interferon with specific regard to the structure of the glycosylated
     molecule. While Biogen believes that the patent will be revoked, if the
     patent were to be upheld and if Rentschler were to obtain, through legal
     proceedings, a determination that the Company's sale of AVONEX(R) in Europe
     infringes a valid Rentschler patent, such result could have a material
     adverse effect on the Company's results of operation and financial
     position.

8.   The Company operates in one segment, which is the business of developing,
     manufacturing and marketing drugs for human health care. The chief
     operating decision makers review the profit and loss of the Company on an
     aggregate basis and manage the operations of the Company as a single
     operating segment. The Company currently derives product revenues from
     sales of its AVONEX(R)(Interferon beta-1a) product for the treatment of
     relapsing forms of multiple sclerosis. The Company also derives revenue
     from royalties on worldwide sales by the Company's licensees of a number of
     products covered under patents controlled by the Company, including alpha
     interferon and hepatitis B vaccines and diagnostic products.


<PAGE>   12


                                                                         Page 12

                          BIOGEN, INC. AND SUBSIDIARIES
                MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL
                       CONDITION AND RESULTS OF OPERATIONS

OVERVIEW

Biogen, Inc. (the "Company" or "Biogen") is a biopharmaceutical company
principally engaged in the business of developing, manufacturing and marketing
drugs for human health care. The Company currently derives revenues from sales
of AVONEX(R) (Interferon beta-la) for the treatment of relapsing forms of
multiple sclerosis ("MS") and from royalties on worldwide sales by the Company's
licensees of a number of products covered under patents controlled by the
Company, including alpha interferon and hepatitis B vaccines and diagnostic
products.

RESULTS OF OPERATIONS

For the quarter ended September 30, 1999, the Company reported net income of $62
million or $0.39 per diluted share as compared to $38 million or $0.24 per
diluted share for the comparable period of 1998. For the nine months ended
September 30, 1999, the Company reported net income of $151 million or $0.96 per
diluted share as compared to $97 million or $0.63 per diluted share for the
comparable period of 1998.

Total revenues for the current quarter were $208 million, as compared to $146
million in the quarter ended September 30, 1998, an increase of $62 million or
42%. Total revenues for the nine months ended September 30, 1999 were $569
million, as compared to $389 million for the same period of 1998, an increase of
$180 million or 46%. The increase in total revenues was primarily due to
increased sales of the Company's product AVONEX(R).

Product sales for the current quarter were $163 million compared to $107 million
for the comparable period in 1998, an increase of $56 million or 52%. Product
sales for the nine months ended September 30, 1999 were $441 million compared to
$271 million for the comparable period in 1998, an increase of $170 million or
63%. The growth in the third quarter and nine month period of 1999 was primarily
due to an increase in the sales volume of AVONEX(R) in the United States and in
the European Union ("EU"). AVONEX(R) sales outside of the United States were
approximately $48 million in the current quarter as compared to approximately
$25 million in the comparable period of 1998, an increase of $23 million or 92%.
AVONEX(R) sales outside of the United States were approximately $126 million in
the nine months ended September 30, 1999 as compared to approximately $56
million in the comparable period of 1998, an increase of $70 million or 125%.

Revenues from royalties for the current quarter were $45 million as compared to
$38 million for the comparable period of 1998, an increase of $7 million or 18%.
Revenues from royalties for the nine months ended September 30, 1999 were $128
million as compared to $119 million for the comparable period of 1998, an
increase of $9 million or 8%. The increases in royalties for the three and nine
month periods of 1999 over the comparable periods of 1998 are primarily a result
of increases in royalties on sales of alpha interferon.


<PAGE>   13


                                                                         Page 13

The Company expects product sales as a percentage of total revenues to continue
to increase in the near term as the Company continues to market AVONEX(R)
worldwide, and expects sales from AVONEX(R) outside the United States to
continue to increase as a percentage of total product sales. The Company,
however, expects to face increasing competition in the MS marketplace from
existing and new MS treatments that may impact sales of AVONEX(R). In the near
term, the Company expects overall sales of licensee products and royalty
revenues to fluctuate depending on changes in sales volumes for specific
products, patent expirations, new licensing arrangements, if any, or other
developments. Licensee sales levels may also fluctuate from quarter to quarter
due to the timing and extent of major events such as new indication approvals or
government sponsored vaccination programs.

Total costs and expenses for the current quarter were $124 million as compared
to $96 million in the quarter ended September 30, 1998, an increase of $28
million or 29%. Total costs and expenses for the nine months ended September 30,
1999 were $349 million as compared to $261 million for the nine months ended
September 30, 1998, an increase of $88 million or 34%.

Cost of sales in the current quarter totaled $28 million, an increase of $9
million from the quarter ended September 30, 1998. Cost of sales in the
nine-month period ended September 30, 1999 totaled $80 million compared to $52
million for the same period in 1998, an increase of $28 million or 54%. Cost of
product sales were $26 million in the third quarter of 1999 compared to $16
million for the same quarter of 1998, an increase of $10 million or 63%. Cost of
product sales were $70 million and $42 million for the nine months of 1999 and
1998, respectively, an increase of $28 million or 67%. Gross margins on product
sales declined slightly to 84% from 85% for the three-month period ended
September 30, 1999 compared to the same period in 1998. Gross margins on product
sales remained constant at 84% for the nine-month periods ended September 30,
1999 and 1998. Cost of royalty revenues for the current quarter was $3 million,
consistent with the cost of royalty revenue in the comparable period of 1998.
Cost of royalty revenues for the nine-month period of 1999 increased to $10
million as compared to $9 million in the comparable period of 1998. Gross
margins on royalty revenue increased to 94% from 92% for the three-month period
ended September 30, 1999, compared to the same period in 1998. Gross margins on
royalty revenue remained constant at 92% for nine-month periods ended September
30, 1999 and 1998, respectively. The Company expects that gross margins on
royalty revenue will fluctuate in the future based on the impact of one-time
royalty and milestone payments.

Research and development expenses for the current quarter were $59 million, an
increase of $10 million or 20% as compared to the quarter ended September 30,
1998. Research and development expenses were $161 million for the nine-month
period ended September 30, 1999, an increase of $33 million or 26% as compared
to the same period in 1998. The increases were primarily due to increases in
clinical trial costs and an increase in the Company's development efforts
relating to research and development programs in its product pipeline. The
Company expects that, in the long-term, research and development expenses will
increase as the Company continues to expand its development efforts with respect
to new products and as it conducts clinical trials of these products.


<PAGE>   14


                                                                         Page 14

On November 2, 1999, the Company announced that it had halted all trials of its
anti-CD40 ligand monoclonal antibody compound while it addresses issues relating
to adverse thrombo-embolic events.

Selling, general and administrative expenses for the current quarter were $36
million, an increase of $9 million or 33% as compared to the quarter ended
September 30, 1998. Selling, general and administrative expenses for the nine
months ended September 30, 1999 were $107 million, an increase of $26 million or
32% from the same period in 1998. The increases were primarily due to higher
selling and marketing expenses related to sales of AVONEX(R), and the impact of
stock option compensation and related expenses. The Company expects that
selling, general and administrative expenses will increase in the near and
long-term as the Company continues to put in place the commercial infrastructure
and sales and marketing organizations necessary to sell AVONEX(R) worldwide.

Other income, net consists primarily of interest income, partially offset by
interest expenses and other non-operating income and expenses. The increase in
other income, net for the three months ended September 30, 1999 compared to the
same period in 1998 was primarily attributable to the increase in interest
income. The decrease in other income, net for the nine months ended September
30, 1999 compared to the same period in 1998 was primarily attributable to a $15
million write-down of certain non-current marketable securities, partially
offset by the increase in interest income.

As part of its strategic product development efforts, the Company invests in
equity securities of certain biotechnology companies with which it has
collaborative agreements. In December of 1996, Biogen purchased approximately
1.5 million shares of Creative BioMolecules, Inc. common stock for $18 million.
In March of 1997, Biogen purchased approximately 670,000 shares of CV
Therapeutics, Inc. common stock for $7 million. In March of 1998, the Company
purchased approximately 435,000 shares of CuraGen common stock for $5 million
and converted 100,000 shares of CuraGen Series E Preferred Stock valued at $1
million to CuraGen common stock. Each of these small emerging companies is
principally engaged in researching, developing or manufacturing drugs for human
health care. In recent periods, the value of these publicly-traded marketable
securities had been negatively impacted by general market conditions for small
cap biotechnology stocks.

As a matter of policy, Biogen determines on a quarterly basis whether a decline
in the fair value of a marketable security is other than temporary. Unrealized
gains and losses on marketable securities are included in other comprehensive
income in shareholders' equity, net of related tax effects. If a decline in the
fair value of a marketable security below the Company's cost basis is determined
to be other than temporary, such marketable security is written down to its
estimated fair value with a charge to current earnings.

Up through and including the assessment at June 30, 1999, the Company concluded
that substantial evidence existed suggesting that the value of the investments
described above would recover to at least the Company's purchase price. Such
evidence included the prospects for favorable clinical trial results, new
product initiatives, and new collaborative agreements. However, given the lack
of any substantial price recovery during the quarter ended June 30, 1999, and
the amount of time elapsed since the decline in value began, the Company
concluded that it had become unclear over what


<PAGE>   15


                                                                         Page 15

period such price recovery would take place. As a result, it was determined that
the positive evidence suggesting that the investments would recover to at least
the Company's purchase price was not sufficient to overcome the presumption that
the current market price of the investments was the best indicator of value at
June 30, 1999. Accordingly, the related unrealized losses of $15 million were
recognized as other expense.

Income tax expense as a percentage of pre-tax income for the quarters ended
September 30, 1999 and 1998 was 33%, respectively. Income tax expense as a
percentage of pre-tax income for the nine months ended September 30, 1999 and
1998 was 33% and 34%, respectively. The effective tax rate varied from U.S.
statutory rates in the three and nine-month periods of 1999 and 1998, primarily
due to increased European sales and to the utilization of research and
development credits. The Company's effective tax rate is expected to continue at
or near the 33% level for the remainder of 1999.

FINANCIAL CONDITION

At September 30, 1999, cash, cash equivalents and short-term marketable
securities were $673 million compared with $517 million at December 31, 1998, an
increase of $156 million. Working capital increased by $192 million to $751
million from December 31, 1998 to September 30, 1999. Net cash provided from
operating activities for the nine-month period ended September 30, 1999 was $163
million, compared with $126 million in the comparable period of 1998. Cash
outflows for the nine-months ended September 30, 1999, included investments in
property and equipment and patents of $47 million. Cash inflows from financing
activities included $134 million from common stock option and purchase plan
activity, including tax benefits related to stock options and $20 million of
proceeds from the sale of put warrants. Cash outflows from financing activities
included $106 million for purchases of 2,000,000 shares of the Company's common
stock under its stock repurchase program and $3 million for repayments of long
term debt.

On February 22, 1999, the Company announced that its Board of Directors has
authorized the repurchase of up to 8 million shares of the Company's common
stock. The repurchased stock will provide the Company with treasury shares for
general corporate purposes, such as stock to be issued under employee stock
option and stock purchase plans. Stock purchases are expected to occur from time
to time through 2000. The stock repurchase program may be discontinued at any
time. To enhance the stock repurchase program, the Company sold put warrants to
and purchased call options from independent third parties covering a large
portion of the shares intended to be repurchased. The outstanding put warrants
permit a net-share settlement at the Company's option.

On October 4, 1999 the Company announced that it had broke ground for its new
research and development center in Cambridge, Massachusetts. The new 210,000
square foot building is expected to be completed in the spring of 2001 at a
total cost of approximately $95 million of which $28 million had been committed
at September 30, 1999. Additionally, the Company is completing plans to build a
large scale manufacturing plant in Raleigh, North Carolina. The Company expects
that construction will be completed at the end of 2001 at a total cost of
approximately $175 million of which $47 million had been committed at September
30, 1999.


<PAGE>   16


                                                                         Page 16

In October 1999 CuraGen Corporation drew down $10 million on the line of
credit extended to CuraGen in connection with a collaborative agreement with the
Company. CuraGen simultaneously converted the borrowings into approximately
611,000 shares of Curagen Common Stock at the then fair value of $16.37 per
share in accordance with the terms of the credit facility.

Several legal proceedings were pending during the current quarter, which involve
the Company. See Note 4 of the Notes to the Condensed Consolidated Financial
Statements. See also Item 1 - Business, "Patents and Other Proprietary Rights"
of the Company's Annual Report on Form 10-K for the fiscal year ended December
31, 1998 for discussions of these legal proceedings.

The Company believes that existing funds and cash generated from operations are
adequate to satisfy its working capital and capital expenditure requirements in
the foreseeable future. However, the Company may seek to raise additional
capital to take advantage of favorable conditions in the market or in connection
with the Company's development activities.

Year 2000 Issues

Year 2000 is the problem resulting from the use of a two-digit date field to
identify the year in computer software. Consequently, computer programs may not
accurately reflect the appropriate date, confusing "00" as the year 1900 rather
than the year 2000. Year 2000 is a pervasive problem affecting many information
technology systems and embedded technologies (e.g. microprocessors in
communications systems) in all companies, in all industries. Failure by the
Company or failure by third parties upon which the Company relies to effectively
address Year 2000 issues could have a material adverse impact on the Company's
financial position or results of operations.

The Company has developed a plan to address the Year 2000 issue. The plan is
segregated into four phases:

1.   Information Collection - Identify all Year 2000 risk areas and assign
accountability.

2.   Assess Risk - Assign each item a category of risk:

     -    Commercial Risk - Has a significant impact on sale, delivery and
          support of AVONEX(R) or a significant impact on the Company's
          financial position or results of operations.

     -    Operational Risk - Has a significant impact on productivity but does
          not materially impact the Company's financial position or results of
          operations.

     -    Convenience Risk - Has a minor impact on productivity and no impact on
          the Company's financial position or results of operations.

3.   Remediate - Fix or replace, test and implement changes required for Year
2000 compliance.

4.   Contingency Plan - Define procedures to be implemented should a disruption
due to Year 2000 occur.


<PAGE>   17


                                                                         Page 17

The Company has completed the first two phases of the project and has completed
the testing and upgrading of all individual software applications and equipment
that fall within the Commercial Risk category. Additionally, approximately 97%
of the software applications and equipment in the Operational and Convenience
Risk categories have been remediated. All of the Company's major software
applications are purchased from major software vendors and the Company performs
only minor customizations to those applications. The Company's major software
providers have attested to Year 2000 compliance. The Company has reviewed its
operations equipment for embedded technologies which may be Year 2000
susceptible and does not believe necessary modifications to be material.

The Company is communicating with its significant vendors and customers to
determine the progress that those vendors and customers are making in
remediating their own Year 2000 issues. The Company is requiring that
significant vendors and customers certify those products and services to be Year
2000 compliant and in some cases is performing on-site reviews.

To date, Year 2000 costs have been immaterial and the Company believes that
future costs will also be immaterial.

The most reasonably likely worst case scenario, if significant Year 2000 issues
arise, is that the Company would execute its contingency plans to produce,
package, and deliver AVONEX(R), resulting in lower productivity. These
contingency plans include producing and maintaining a sufficient level of
inventory of AVONEX(R) in both bulk and packaged format, developing secondary
sources of packaging and delivery, providing for manual and backup processes.
Customers anticipating Year 2000 concerns, could increase their inventory of
AVONEX(R) prior to the end of the year causing short-term temporary volatility
in sales between periods. Additionally, third parties from whom the Company
receives royalty revenues could encounter difficulties in their efforts to
produce and sell products which generate royalty revenue for the Company.

OUTLOOK

Safe Harbor Statement under Private Securities Litigation Reform Act of 1995

In addition to historical information, this quarterly report on Form 10-Q
contains forward-looking statements that involve risks and uncertainties that
could cause actual results to differ materially from those reflected in such
forward-looking statements. Reference is made in particular to forward-looking
statements regarding the anticipated level of future royalty revenues, product
sales, expenses and profits, predictions as to the anticipated outcome of
pending litigation and opposition proceedings, statements regarding the
anticipated costs and completion dates related to the Company's building
activities and statements regarding the expected outcome of planned measures to
deal with Year 2000 issues. These and all other forward-looking statements are
made based on the Company's current belief as to the outcome and timing of such
future events. Factors which could cause actual results to differ from the
Company's expectations and which could negatively impact the Company's results
of operations are discussed below and elsewhere in this Management's Discussion
and Analysis of Financial Condition and Results of Operations.


<PAGE>   18


                                                                         Page 18

Dependence on AVONEX(R) Sales and Royalty Revenue

The Company's ability to sustain increases in revenues and profitability in the
near term will be primarily dependent on the level of revenues and profitability
from AVONEX(R) sales. The Company's ability to sustain profitability from sales
of AVONEX(R) will depend on a number of factors, including: continued market
acceptance of AVONEX(R) worldwide; the Company's ability to maintain a high
level of patient satisfaction with AVONEX(R); the nature of regulatory and
pricing decisions related to AVONEX(R) worldwide and the extent to which
AVONEX(R) receives and maintains reimbursement coverage; successful resolution
of the lawsuit with Berlex related to the "McCormick" patents, which if decided
in Berlex's favor could have a material adverse effect on the Company's
financial position and results of operations; success in revoking the Rentschler
patent since if the patent were to be upheld and if Rentschler were to obtain,
through legal proceedings, a determination that the Company's sale of AVONEX(R)
in Europe infringes a valid Rentschler patent, such result could have a material
adverse effect on the Company's results of operation and financial condition;
the Company's ability to sustain market share of AVONEX(R) in light of the
impact of competitive products for the treatment of multiple sclerosis; the
success of ongoing development work related to AVONEX(R) in expanded multiple
sclerosis indications and the continued accessibility of third parties to vial,
label, and distribute AVONEX(R) on acceptable terms. The Company also receives
royalty revenues which contribute significantly to its overall profitability.
The Company's ability to maintain the level of its royalty revenues will depend
on a number of factors. For example, pricing reforms, health care reform
initiatives, other legal and regulatory developments and the introduction of
competitive products may have an impact on product sales by the Company's
licensees. In addition, licensee sales levels may fluctuate from quarter to
quarter due to the timing and extent of major events such as new indication
approvals or government sponsored vaccination programs. Since the Company is not
involved in the development or sale of products by licensees, the Company is
unable to predict the timing or potential impact of factors which may affect
licensee sales. In the long term, the Company expects its royalty revenue to be
affected most significantly by patent expirations.

There can be no assurance that the Company will achieve a positive outcome with
respect to any of the factors discussed in this Section or that the timing and
extent of the Company's success with respect to any combination of these factors
will be sufficient to result in sustained increases in revenues or profitability
or the sustained profitability of the Company. For a further discussion of risks
regarding drug development, patent matters, including the Berlex lawsuit on the
"McCormick" patents, competition in the multiple sclerosis market and regulatory
matters, see the Company's Annual Report on Form 10-K for the period ended
December 31, 1998 under the headings "Business - Risks Associated with Drug
Development", "Business - Patents and Other Proprietary Rights", "Business -
Competition and Marketing - AVONEX(R) (interferon beta-la)", "Business -
Regulation", "Legal Proceedings" and "Management's Discussion and Analysis of
Financial Condition and Results of Operations - Outlook."


<PAGE>   19


                                                                         Page 19

New Products

AVONEX(R) is currently the only product sold by the Company. The Company's
long-term viability and growth will depend on the successful development and
commercialization of other products from its research activities and
collaborations. The Company is continuing to expand its development efforts
related to other potential products in its pipeline. The expansion of the
pipeline may include increases in spending on internal projects, the acquisition
of third party technologies or products or other types of investments. Product
development involves a high degree of risk. Only a small number of research and
development programs result in the commercialization of a product. Success in
preclinical and early clinical trials does not ensure that later stage or large
scale clinical trials will be successful. Many important factors affect the
Company's ability to successfully develop and commercialize drugs, including the
ability to obtain and maintain necessary patents and licenses, to demonstrate
safety and efficacy of drug candidates at each stage of the clinical trial
process, to meet applicable regulatory standards and to receive required
regulatory approvals, to be capable of producing drug candidates in commercial
quantities at reasonable costs, to compete successfully against other products
and to market products successfully. There can be no assurance that the Company
will be successful in its efforts to develop and commercialize new products.


<PAGE>   20


                                                                         Page 20

PART II - OTHER INFORMATION

Item 6 - Exhibits and Reports on Form 8-K

(a)  Exhibits

     No. 27    Financial Data Schedule (for EDGAR filing purposes only).


<PAGE>   21


                                                                         Page 21

SIGNATURES

Pursuant to the requirements 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.

Dated: November 15, 1999                            /s/Timothy M. Kish
                                                    ----------------------------
                                                    Timothy M. Kish
                                                    Vice President-Finance and
                                                    Chief Financial Officer



EXHIBITS

Index to Exhibit.



     No. 27    Financial Data Schedule (for EDGAR filing purposes only).