<PAGE>   1

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549



                                    FORM 10-Q

             QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE
                         SECURITIES EXCHANGE ACT OF 1934



                FOR THE QUARTERLY PERIOD ENDED SEPTEMBER 30, 2000



                         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
     incorporation or organization)                    Identification No.)


                    14 CAMBRIDGE CENTER, CAMBRIDGE, MA 02142
                                 (617) 679-2000
                   (Address, including zip code, and telephone
                  number, including area code, of registrant's
                          principal executive offices)


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 [ ]

The number of shares of the registrant's Common Stock, $0.01 par value,
outstanding as of October 30, 2000 was 147,919,983 shares.



                                       1
<PAGE>   2

                                  BIOGEN, INC.

                                      INDEX

                                                                           PAGE
PART I - FINANCIAL INFORMATION                                            NUMBER

Condensed Consolidated Statements of Income - Three and nine months
    ended September 30, 2000 and 1999                                        3

Condensed Consolidated Balance Sheets - September 30, 2000 and
    December 31, 1999                                                        4

Condensed Consolidated Statements of Cash Flows -
    Nine months ended September 30, 2000 and 1999                            5

Notes to Condensed Consolidated Financial Statements                         6

Management's Discussion and Analysis of Financial Condition and
    Results of Operations                                                   10

PART II - OTHER INFORMATION                                                 16



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


                                       2
<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,
                                                2000         1999         2000         1999
                                              --------     --------     --------     --------
<S>                                           <C>          <C>          <C>          <C>
REVENUES:

    Product                                   $193,242     $163,448     $557,847     $440,620
    Royalties                                   40,512       44,983      123,269      128,460
                                              --------     --------     --------     --------

Total revenues                                 233,754      208,431      681,116      569,080
                                              --------     --------     --------     --------

COSTS AND EXPENSES:

    Cost of revenues                            33,027       28,498       92,445       80,329
    Research and development                    94,498       58,958      229,205      160,886
    Selling, general and administrative         41,745       36,484      123,849      107,344
                                              --------     --------     --------     --------

Total costs and expenses                       169,270      123,940      445,499      348,559
                                              --------     --------     --------     --------

Income from operations                          64,484       84,491      235,617      220,521
Other income, net                               33,204        8,092      148,965        5,006
                                              --------     --------     --------     --------

INCOME BEFORE INCOME  TAXES                     97,688       92,583      384,582      225,527
Income taxes                                    29,307       30,554      122,775       74,426
                                              --------     --------     --------     --------

NET INCOME                                    $ 68,381     $ 62,029     $261,807     $151,101
                                              ========     ========     ========     ========

BASIC EARNINGS PER SHARE                      $   0.46     $   0.41     $   1.76     $   1.01
                                              ========     ========     ========     ========
DILUTED EARNINGS PER SHARE                    $   0.44     $   0.39     $   1.69     $   0.96
                                              ========     ========     ========     ========

SHARES USED IN COMPUTING:
Basic earnings per share                       148,074      150,108      149,026      149,851
                                              ========     ========     ========     ========
Diluted earnings per share                     153,702      158,198      155,188      157,768
                                              ========     ========     ========     ========
</TABLE>



            See Notes to Condensed Consolidated Financial Statements.


                                       3
<PAGE>   4

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


                                              September 30,     December 31,
                                                  2000             1999
                                              -------------     ------------
                                               (unaudited)
ASSETS
Current assets
    Cash and cash equivalents                  $    35,849      $    56,920
    Marketable securities                          623,185          597,619
    Accounts receivable, net                       145,690          137,363
    Deferred tax assets                             56,279           50,565
    Other current assets                            68,237           67,759
                                               -----------      -----------
    Total current assets                           929,240          910,226
                                               -----------      -----------

Property, plant and equipment
    Cost                                           479,701          351,566
    Less accumulated depreciation                  128,997          111,789
                                               -----------      -----------
    Property, plant and equipment, net             350,704          239,777
                                               -----------      -----------

Patents, net                                        13,415           13,871
Marketable securities                               86,780           98,017
Other assets                                        22,917           16,082
                                               -----------      -----------

                                               $ 1,403,056      $ 1,277,973
                                               ===========      ===========

LIABILITIES AND SHAREHOLDERS' EQUITY
Current liabilities
    Accounts payable                           $    20,382      $    30,125
    Current portion of long-term debt                4,888            4,888
    Accrued expenses and other                     210,542          155,257
                                               -----------      -----------
    Total current liabilities                      235,812          190,270
                                               -----------      -----------

Long-term debt, less current portion                48,824           52,073
Other long-term liabilities                         57,214           56,100
Commitments and contingencies                            -                -

Shareholders' equity
    Common stock                                     1,516            1,507
    Additional paid-in capital                     767,229          676,673
    Retained earnings                              472,328          352,016
    Accumulated other comprehensive income          34,400           45,618
    Treasury stock, at cost                       (214,267)         (96,284)
                                               -----------      -----------

Total shareholders' equity                       1,061,206          979,530
                                               -----------      -----------
                                               $ 1,403,056      $ 1,277,973
                                               ===========      ===========



            See Notes to Condensed Consolidated Financial Statements.


                                       4
<PAGE>   5

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

<TABLE>
<CAPTION>
                                                                         Nine Months Ended
                                                                           September 30,
                                                                       2000           1999
                                                                     ---------      ---------
<S>                                                                  <C>            <C>
CASH FLOWS FROM OPERATING ACTIVITIES
    Net income                                                       $ 261,807      $ 151,101
    Adjustments to reconcile net income to
       net cash provided from operating activities:
       Depreciation and amortization                                    21,884         22,563
       Deferred income taxes                                               216          1,711
       Other                                                             2,681          1,610
       Gain on sale of non-current marketable securities              (101,129)             -
       Write-down of non-current marketable securities                       -         15,287
       Changes in:
           Accounts receivable                                          (8,327)       (28,582)
           Other current and other assets                              (32,024)         1,116
           Accounts payable, accrued expense and
              other current and long-term liabilities                   45,999         (1,969)
                                                                     ---------      ---------
    Net cash from operating activities                                 191,107        162,837
                                                                     ---------      ---------

CASH FLOWS FROM INVESTING ACTIVITIES
    Purchases of marketable securities                                (530,518)      (468,988)
    Proceeds from sales and maturities of marketable securities        505,894        356,681
    Proceeds from sales of non-current marketable securities           120,199              -
    Acquisitions of property and equipment                            (132,655)       (43,845)
    Additions to patents                                                (3,316)        (2,927)
                                                                     ---------      ---------
       Net cash from investing activities                              (40,396)      (159,079)
                                                                     ---------      ---------

CASH FLOWS FROM FINANCING ACTIVITIES
    Payments of long-term debt                                          (3,249)        (3,249)
    Purchases of treasury stock                                       (280,406)      (106,453)
    Proceeds from put warrants                                               -         19,947
    Issuance of common stock, stock option exercises and related
       tax benefits                                                    111,873        134,046
                                                                     ---------      ---------
       Net cash from investing activities                             (171,782)        44,291
                                                                     ---------      ---------

NET INCREASE/(DECREASE) IN CASH AND CASH EQUIVALENTS                   (21,071)        48,049

CASH AND CASH EQUIVALENTS, BEGINNING OF PERIOD                          56,920         25,445
                                                                     ---------      ---------

CASH AND CASH EQUIVALENTS, END OF PERIOD                             $  35,849      $  73,494
                                                                     =========      =========
</TABLE>


         See Notes to Condensed Consolidated Financial Statements.


                                       5
<PAGE>   6

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

1.  BASIS OF PRESENTATION

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 the
Consolidated Financial Statements in the Company's 1999 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.

INVENTORIES

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

<TABLE>
<CAPTION>
                                             September 30,    December 31,
(in thousands)                                   2000            1999
                                             -------------    ------------

<S>                                          <C>              <C>
Raw materials                                  $  5,491         $  5,679
Work in process                                  14,304           15,110
Finished goods                                   16,597           19,242
                                               --------         --------
                                               $ 36,392         $ 40,031
                                               ========         ========
</TABLE>

2.  FINANCIAL INSTRUMENTS

On June 15, 1998, the Financial Accounting Standards Board issued Statement of
Financial Accounting Standards No. 133, "Accounting for Derivative Instruments
and Hedging Activities" ("SFAS 133"). The Company elected to adopt SFAS 133 in
the fourth quarter of 1998. All derivatives are recognized on the balance sheet
at their fair value. Changes in the fair value of derivatives are recorded each
period in current earnings or other comprehensive income, depending on whether a
derivative is designated as part of a hedge transaction and, if it is, the type
of hedge transaction. The Company assesses, both at its inception and on an
on-going basis, whether the derivatives that are used in hedging transactions
are highly effective in offsetting the changes in cash flows of hedged items.
The Company assesses hedge ineffectiveness on a quarterly basis and records the
gain or loss related to the ineffective portion to current earnings to the
extent significant. If the Company determines that a hedged forecasted
transaction is no longer probable of occurring, the Company discontinues hedge
accounting for the affected portion of the transaction, and any unrealized gain
or loss on the contract is recognized in current earnings.

As of September 30, 2000, the Company had $16.7 million outstanding under a
floating rate loan secured by the Company's laboratory and office building in
Cambridge, Massachusetts and $37.0 million outstanding under a floating rate
loan agreement for financing the construction of its biological manufacturing
facility in North Carolina. The Company uses interest rate swap agreements to
mitigate the risk associated with its floating rate debt. The fair value of the
interest rate swap agreements at September 30, 2000, representing the cash
requirements of the Company to settle the agreements, was approximately


                                       6
<PAGE>   7
$291,000, and was included in accrued expenses and other. The Company has
designated the interest rate swaps as cash flow hedges. There were no amounts of
hedge ineffectiveness related to the Company's interest rate swaps during the
three and nine months ended September 30, 2000 or in the comparable period of
1999, and no gains or losses were excluded from the assessment of hedge
effectiveness. The Company records the differential to be paid or received on
the interest rate swaps as incremental interest expense.

The Company has foreign currency forward contracts to hedge specific forecasted
transactions denominated in foreign currencies. All foreign currency forward
contracts have durations of 90 days to 18 months. These contracts have been
designated as cash flow hedges and accordingly, to the extent effective, any
unrealized gains or losses on these foreign currency forward 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 foreign currency forward contracts outstanding
at September 30, 2000 was approximately $99.0 million. These contracts had a
fair value of approximately $14.0 million, representing an unrealized gain, and
was included in other current assets at September 30, 2000.

For the three and nine months ended September 30, 2000 and 1999, there were no
significant amounts recognized in earnings due to hedge ineffectiveness for
outstanding foreign currency forward contracts. For the three and nine months
ended September 30, 2000, approximately $585,620 and $977,224, respectively, in
gains were recognized as a result of the discontinuance of cash flow hedge
accounting because it was no longer probable that the hedge forecasted
transaction would occur. For the three and nine months ended September 30, 1999,
there were no significant amounts recognized as a result of the discontinuance
of cash flow hedge accounting because it was no longer probable that the hedge
forecasted transaction would occur. The Company recognized $4.1 million and $8.8
million of gains in product revenue for the settlement of certain effective cash
flow hedge instruments for the three and nine months ended September 30, 2000,
respectively. The Company recognized $1.3 million and $2.4 million of gains in
royalty revenue for the settlement of certain effective cash flow hedge
instruments for the three and nine months ended September 30, 2000,
respectively. For the three and nine months ended September 30, 1999, the
Company recognized $1.7 million and $4.5 million of gains in product revenue for
the settlement of certain cash flow hedge instruments, respectively. For the
three and nine months ended September 30, 1999, the Company recognized $429,000
and $1.7 million, respectively, of gains in royalty revenue for the settlement
of certain cash flow hedge instruments during the period. These settlements were
recorded in the same period as the related forecasted transactions affected
earnings.

3.  COMPREHENSIVE INCOME

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, net of tax and certain
derivative instruments, net of tax. Comprehensive income for the three months
ended September 30, 2000 and 1999 was $73.2 million and $62.6 million,
respectively. Comprehensive income for the nine months ended September 30, 2000
and 1999 was $250.6 million and $169.8 million, respectively.

4.  EARNINGS PER SHARE

The Company calculates earnings per share in accordance with Statement of
Financial Accounting Standards No. 128, "Earnings per Share". Basic earnings per
share is computed by dividing the net income available to common shareholders by
the weighted average number of shares of common stock outstanding. For purposes
of calculating diluted earnings per share the denominator includes both the
weighted average number of shares of common stock outstanding and the number of
dilutive common stock equivalents such as stock options and warrants. Options to
purchase approximately 1.8 million shares were outstanding at September 30, 2000
but not included in the computation of diluted earnings per share because the
exercise prices of the options were greater than the average market price of the
Company's common stock during the period. The put warrants sold in connection
with the Company's stock repurchase program did not have a material additional
dilutive effect.


                                       7
<PAGE>   8

Shares used in calculating basic and diluted earnings per share are as follows:

<TABLE>
<CAPTION>
                                       Three Months Ended       Nine Months Ended
                                          September 30,           September 30,
(in thousands)                          2000        1999        2000        1999
                                       -------     -------     -------     -------
<S>                                    <C>         <C>         <C>         <C>
Weighted average number of shares
    of common stock outstanding        148,074     150,108     149,026     149,851
Dilutive stock options                   5,628       8,090       6,162       7,917
                                       -------     -------     -------     -------
Shares used in calculating diluted
    earnings per share                 153,702     158,198     155,188     157,768
                                       =======     =======     =======     =======
</TABLE>


5.  SHARE REPURCHASE PROGRAM

On February 22, 1999, the Company announced that its Board of Directors
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. During the first nine months of 2000, the Company repurchased
approximately 4.3 million shares of its common stock at a cost of $280.4
million.

To enhance the 1999 stock repurchase program, the Company sold put warrants to
and purchased call options from independent third parties for a total of 4
million shares, of which 400,000 were outstanding at September 30, 2000 at a
strike price of $49.47. All of the Company's put warrants outstanding are
exercisable only at the date of expiration, with expiration dates ranging from
October through November of 2000. The outstanding put warrants permit a
net-share settlement at the Company's option and, therefore, did not result in a
put obligation on the Company's Consolidated Balance Sheets.

6.  OTHER INCOME, NET

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

<TABLE>
<CAPTION>
                              Three Months Ended           Nine Months Ended
                                September 30,                September 30,
                            ---------------------      -----------------------
                              2000         1999          2000           1999
                            --------      -------      ---------      --------

<S>                         <C>           <C>          <C>            <C>
Interest income             $ 11,067      $ 9,450      $  32,174      $ 25,713
Interest expense              (1,100)      (1,171)        (3,285)       (3,527)
Other income (expense)        23,237         (187)       120,076       (17,180)
                            --------      -------      ---------      --------

Total other income, net     $ 33,204      $ 8,092      $ 148,965      $  5,006
                            ========      =======      =========      ========
</TABLE>

During the three months ended September 30, 2000, the Company realized gains of
approximately $24.1 million upon the acquisition by third parties of two of the
companies in which the Company had invested in separate business combinations.
Additionally, other income for the nine months ended September 30, 2000 included
gains on the sale of certain non-current marketable securities totaling
approximately $101.1 million. Other expense for the nine months ended September
30, 1999 included a $15.3 million write-down of certain non-current marketable
securities. The Company had determined that the decline in fair value below cost
of the marketable securities was other than temporary.

7.  INCOME TAX EXPENSE

Income tax expense as a percentage of pre-tax income for the three months ended
September 30, 2000 and 1999 was approximately 30% and 33%, respectively. Income
tax expense as a percentage of pre-tax income


                                       8
<PAGE>   9
for the nine months ended September 30, 2000 and 1999 was approximately 32% and
33%, respectively. During the three and nine months ended September 30, 2000,
the Company recognized gains relating to certain non-current marketable
securities. Excluding the tax effect on these gains the Company's effective tax
rate for the three and nine months ended September 30, 2000 was approximately
30%. The effective tax rate varied from the U.S. statutory rates for the first
nine months of 2000 and 1999 primarily due to increasing European sales and to
the utilization of research and development credits. The Company's effective tax
rate outside the U.S. is lower than the U.S. tax rate, and the Company expects
that the U.S. tax rate will decline as a percentage of its total tax rate as
international sales increase.

8.  LITIGATION

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 (U.S. Patent No.
5,376,567) in the United States in the production of Biogen's AVONEX(R)
(Interferon beta-1a) product. In November 1996, Berlex's New Jersey action was
transferred to the United States District Court in Massachusetts and
consolidated for pre-trial purposes with a related declaratory judgment 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 related to the McCormick patent (U.S. Patent
No. 5,795,779). On September 23, 1998, the cases were consolidated for pre-trial
and trial purposes. Berlex sought a judgment granting it damages, a trebling of
any damages awarded and a permanent injunction restraining Biogen from the
alleged infringement. A hearing on the parties' summary judgment motions in the
case was completed in March 2000. In September 2000, the District Court rendered
final judgment in favor of Biogen and against Berlex determining that Biogen's
production of AVONEX(R) did not infringe any of the claims of the Berlex
patents. Berlex has appealed this decision with the Court of Appeals for the
Federal Circuit. An unfavorable ruling on appeal would result in the case being
remanded to the District Court for trial. If Berlex were to be successful in its
appeal and the case were remanded, an unfavorable ruling in the remanded case
could have a material adverse effect on the Company's results of operations and
financial position. The Company believes that the decision of the District Court
that Biogen does not infringe the Berlex patents is sound, but the ultimate
outcome of the appeal is not currently determinable. As a result, an estimate of
any potential loss or range of loss cannot be made at this time.

In 1995, the Company filed an opposition with the Opposition Division of the
European Patent Office to oppose a European patent (the "Rentschler I Patent")
issued to Dr. Rentschler Biotechnologie GmbH ("Rentschler") relating to
compositions of matter of beta interferon. In 1997, the European Patent Office
issued a decision to revoke the Rentschler I Patent. Rentschler has appealed
that decision and the appeal is still pending. A hearing on the appeal has been
scheduled for December 2000. On October 13, 1998, the Company filed another
opposition with the Opposition Division of the European Patent Office to oppose
a second European patent issued to Rentschler (the "Rentschler II Patent") with
certain claims regarding compositions of matter of beta interferon with specific
regard to the structure of the glycosylated molecule. A hearing on the Company's
opposition previously scheduled for October 2000 has been postponed, and will
likely be held in 2001. While Biogen believes that the Rentschler II Patent will
be revoked and that the revocation of the Rentschler I Patent will be upheld on
appeal, if either the Rentschler I Patent or the Rentschler II 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.

9.  SEGMENT INFORMATION

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. Accordingly, the Company operates in one segment, which is
the business of developing, manufacturing and marketing drugs for human health
care. 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.

10.  NEW ACCOUNTING PRONOUNCEMENT

In December 1999, the United States Securities and Exchange Commission issued
Staff Accounting Bulletin 101, "Revenue Recognition in Financial Statements"
("SAB 101"). SAB 101 provides the staff's views in applying generally accepted
accounting principles to selected revenue recognition issues, as well as
examples of how the staff applies revenue recognition to specific circumstances.
The Company is currently assessing the impact, if any; however, the Company does
not currently anticipate that SAB 101 will have a material effect on the
Company's financial position and results of operations.


                                       9
<PAGE>   10

                          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 its AVONEX(R) (Interferon beta-1a) product for the treatment of relapsing
forms of multiple sclerosis ("MS"). 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.

RESULTS OF OPERATIONS

For the quarter ended September 30, 2000, the Company reported net income of
$68.4 million or $0.44 per diluted share as compared to $62.0 million or $0.39
per diluted share for the comparable period of 1999. For the nine months ended
September 30, 2000, the Company reported net income of $261.8 million or $1.69
per diluted share as compared to $151.1 million or $0.96 per diluted share for
the comparable period of 1999.

Total revenues for the quarter ended September 30, 2000 were $233.8 million, as
compared to $208.4 million in the same period of 1999, an increase of $25.4
million or approximately 12%. Total revenues for the nine months ended September
30, 2000 were $681.1 million, as compared to $569.1 million in the same period
of 1999, an increase of $112 million or approximately 20%.

Product revenues in the current quarter were $193.2 million as compared to
$163.4 million for the same period of 1999, an increase of $29.8 million or
approximately 18%. Product revenues in the nine months ended September 30, 2000
were $557.8 million as compared to $440.6 million for the same period of 1999,
an increase of $117.2 million or approximately 27%. Product revenues from
AVONEX(R) represent approximately 83% of the Company's total revenues in the
current quarter as compared to 78% for the same period of 1999. Product revenues
from AVONEX(R) represent approximately 82% of the Company's total revenues in
the nine months ended September 30, 2000 as compared to 77% for the same period
of 1999. The growth in product revenues in the three and nine month periods
ended September 30, 2000 over the comparable periods in 1999 was primarily
attributable to increases in the sales volume of AVONEX(R) in the United States
and in the fifteen member countries of the European Union ("EU"). AVONEX(R)
sales outside of the United States were approximately $55 million and $154.5
million, respectively in the three and nine months ended September 30, 2000 as
compared to $48 million and $126.1 million in the same periods of 1999,
respectively.

Revenues from royalties in the three months ended September 30, 2000 were $40.5
million, a decrease of $4.5 million or approximately 10% as compared to $45
million of royalty revenue for the same period in 1999. Revenues from royalties
in the nine months ended September 30, 2000 were $123.3 million, a decrease of
approximately 4% as compared to $128.5 million of royalty revenue for the same
period in 1999. Revenues from royalties represented approximately 17% and 18%,
respectively, of total revenues for the three and nine months ended September
30, 2000 as compared to 22% and 23%, respectively, for the same periods in 1999.

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. 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 and long term, the Company expects its royalty revenue to
be affected most significantly by patent expirations. See "Business - Patents
and Other Proprietary Rights" of the


                                       10
<PAGE>   11

Company's Annual Report on Form 10-K for the fiscal year ended December 31,
1999. In the near term, Biogen's royalty revenues may also be significantly
affected as a result of a potential dispute with Schering Plough over twelve to
eighteen months of royalties payable by Schering Plough on U.S. sales of
INTRON(R) A. See "Outlook - Dependence on AVONEX(R) Sales and Royalty Revenue."
In addition, sales levels of products sold by the Company's licensees may
fluctuate from quarter to quarter due to the timing and extent of major events
such as new indication approvals or government sponsored programs.

COSTS AND EXPENSES

Total costs and expenses for the three months ended September 30, 2000 were
$169.3 million as compared to $123.9 million in the same period of 1999, an
increase of approximately 37%. Total costs and expenses for the nine months
ended September 30, 2000 were $445.5 million as compared to $348.6 million in
the same period of 1999, an increase of approximately 28%.

Cost of revenues in the three months ended September 30, 2000 totaled $33
million compared to $28.5 million in the same period of 1999, an increase of
$4.5 million or 16%. Cost of revenues in the nine months ended September 30,
2000 totaled $92.4 million compared to $80.3 million in the same period of 1999,
an increase of $12.1 million or 15%. The increase in cost of revenues was
attributable to the higher sales volume of AVONEX(R). Included in cost of
revenues for the three months ended September 30, 2000 and 1999 is $29.9 million
and $25.8 million, respectively, of costs related to product revenues and $3.2
million and $2.7 million, respectively, of costs related to royalty revenue.
Included in cost of revenues for the nine months ended September 30, 2000 and
1999 is $83.4 million and $70 million, respectively, of costs related to product
revenues and $9 million and $10.3 million, respectively, of costs related to
royalty revenue. Gross margins on product revenues increased to approximately
85% for the three months and nine months ended September 30, 2000 compared to
84% in the same periods in 1999. Gross margins on royalty revenue decreased to
approximately 92% for the three months ended September 30, 2000 compared to 94%
in the same period in 1999. Gross margins on royalty revenue increased to
approximately 93% for the nine months ended September 30, 2000 compared to 92%
in the same period in 1999. The Company expects that gross margins on royalty
revenue will fluctuate in the future based on changes in sales volumes for
specific products.

Research and development expenses in the current quarter were $94.5 million, an
increase of $35.5 million or 60% as compared to $59 million in the same period
of 1999. Research and development expenses in the nine months ended September
30, 2000 were $229.2 million, an increase of $68.3 million or 42% as compared to
$160.9 million in the same period of 1999. The increases were primarily due to
up-front costs associated with new collaborative efforts of approximately $21.4
million, an increase in clinical trial costs and the costs associated with an
increase in the Company's other development efforts related to its ongoing
research and development programs. The Company expects that, in the near and
long-term, research and development expenses will increase as the Company
continues to expand its development efforts with respect to new products,
conducts clinical trials of these products and continues work on new
formulations and delivery methods for AVONEX(R).


                                       11
<PAGE>   12

Selling, general and administrative expenses in the third quarter of 2000 were
$41.7 million, an increase of $5.3 million or 14% as compared to the same period
of 1999. Selling, general and administrative expenses in the nine months ended
September 30, 2000 were $123.8 million, an increase of $16.5 million or 15%
compared to the same period of 1999. This increase was primarily due to an
increase in selling and marketing expenses related to the sale of AVONEX(R). The
Company expects that selling, general and administrative expenses will continue
to increase in the near term as the Company continues to expand its sales and
marketing organizations and efforts necessary to sell AVONEX(R) worldwide.

OTHER INCOME, NET

Other income, net consists primarily of interest income, partially offset by
interest expenses and other non-operating income and expenses. Other income, net
in the third quarter of 2000 was $33.2 million as compared to $8.1 million in
the same period in 1999, an increase of $25.1 million. Other income, net in the
nine months ended September 30, 2000 was $149 million as compared to $5 million
in the same period in 1999, an increase of $144 million. Interest income for the
three months ended September 30, 2000 was $11.1 million compared to $9.5 million
in the same period of 1999, an increase of $1.6 million or 17%. Interest income
for the nine months ended September 30, 2000 was $32.2 million compared to $25.7
million in the same period of 1999, an increase of $6.5 million or 25%. The
increase in interest income for the three and nine months ended September 30,
2000 is due primarily to an increase in funds invested and an increase interest
rates. In the three months ended September 30, 2000 and 1999 interest expense
was $1.1 million and $1.2 million, respectively. In the nine months ended
September 30, 2000 interest expense was $3.3 million compared to $3.5 million in
the same period in 1999. Other non-operating income (expense) increased by $23.4
million in the three months ended September 30, 2000 from the same period in
1999. Other non-operating income (expense) increased by $137.3 million in the
nine months ended September 30, 2000 from the same period in 1999. The increase
in non-operating income is due primarily to gains on certain non-current
marketable securities of approximately $24.1 million and $125.3 million in the
three and nine months ended September 30, 2000. Additionally, other expense in
the nine months ended September 30, 1999 included the write-down of certain
non-current marketable securities totaling $15.3 million. The Company expects
interest income to vary based on changes in the amount of funds invested and
fluctuations in interest rates.

INCOME TAXES

Income tax expense as a percentage of pre-tax income for the three months ended
September 30, 2000 and 1999 was approximately 30% and 33%, respectively. Income
tax expense as a percentage of pre-tax income for the nine months ended
September 30, 2000 and 1999 was approximately 32% and 33%, respectively. During
the three and nine months ended September 30, 2000, the Company recognized gains
on certain non-current marketable securities. Excluding the tax effect on these
gains the Company's effective tax rate for the three and nine months ended
September 30, 2000 was approximately 30%. The effective tax rate varied from the
U.S. statutory rates for the first nine months of 2000 and 1999 primarily due to
increasing European sales and to the utilization of research and development
credits. The Company's effective tax rate outside the U.S. is lower than the
U.S. tax rate, and the Company expects that the U.S. tax rate will decline as a
percentage of its total tax rate as international sales increase.

FINANCIAL CONDITION

At September 30, 2000, cash, cash equivalents and short-term marketable
securities were $659 million compared with $654.6 million at December 31, 1999,
an increase of $4.4 million. Working capital decreased $26.5 million to $693.4
million. Net cash from operating activities for the nine month period ended
September 30, 2000 was $191.1 million compared with $162.8 million for the same
period in 1999. Significant cash inflows from investing activities during the
first nine months of 2000 included $120.2 million in proceeds from the sale of
certain non-current marketable securities. Cash outflows during the first nine
months of 2000 included investments in property and equipment and patents of
$136 million. Significant cash outflows from financing activities included
$280.4 million for purchases of the Company's common stock under its stock
repurchase program and $3.2 million for repayments on loan agreements


                                       12
<PAGE>   13

with banks. Cash inflows included $111.9 million from common stock option
exercises and related tax benefits and employee stock purchase plan activity.

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. During the first nine months of 2000, the Company repurchased
approximately 4.3 million shares of its common stock at a cost of $280.4
million.

To enhance the 1999 stock repurchase program, the Company sold put warrants to
and purchased call options from independent third parties for a total of 4
million shares, of which 400,000 were outstanding at September 30, 2000 at a
strike price of $49.47. All of the Company's put warrants outstanding are
exercisable only at the date of expiration, with expiration dates ranging from
October through November of 2000. The outstanding put warrants permit a
net-share settlement at the Company's option and, therefore, did not result in a
put obligation on the Company's Consolidated Balance Sheets.

On October 4, 1999, the Company began construction of its new research and
development center in Cambridge, Massachusetts. The new 224,000 square foot
building is expected to be completed in the spring of 2001 at a total cost of
approximately $95 million, of which $86 million had been committed at September
30, 2000. Additionally, the Company is building a large scale manufacturing
plant in Research Triangle Park, 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 $137 million had been committed at
September 30, 2000.

Several legal proceedings were pending during the current quarter which involve
the Company. See Note 8 of the Notes to the Condensed Consolidated Financial
Statements.

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 raise additional capital to
take advantage of favorable conditions in the market or in connection with the
Company's development activities.

NEW ACCOUNTING PRONOUNCEMENT

In December 1999, the United States Securities and Exchange Commission issued
Staff Accounting Bulletin 101, "Revenue Recognition in Financial Statements"
("SAB 101"). SAB 101 provides the staff's views in applying generally accepted
accounting principles to selected revenue recognition issues, as well as
examples of how the staff applies revenue recognition guidance to specific
circumstances. The Company is currently assessing the impact, if any; however,
the Company does not currently anticipate that SAB 101 will have a material
effect on the Company's financial position and results of operations.


                                       13
<PAGE>   14
OUTLOOK

SAFE HARBOR STATEMENT UNDER PRIVATE SECURITIES LITIGATION REFORM ACT OF 1996

In addition to historical information, this quarterly report 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 product sales, royalty revenues,
expenses and profits and predictions as to the anticipated outcome of pending
litigation and patent-related proceedings. 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
financial condition and results of operations are discussed below and elsewhere
in this Management's Discussion and Analysis of Financial Condition and Results
of Operations.

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; the Company's ability
to sustain market share of AVONEX(R) in light of the impact of competitive
products for the treatment of MS; the success of ongoing development work
related to AVONEX(R) in expanded MS indications and the continued accessibility
of third parties to vial, label, and distribute AVONEX(R) on acceptable terms.
The Company's level of revenue related to AVONEX(R) may also depend on the
Company's continued success in its litigation with Berlex on the "McCormick"
patents which has been decided in Biogen's favor, but which if Biogen were to
lose on appeal would be remanded to the District Court for trial, and if
ultimately decided in Berlex's favor could have a material adverse effect on the
Company's results of operations and financial condition. Another factor which
could impact AVONEX(R) revenues will be the outcome of the Company's efforts to
revoke the Rentschler patents since if the patents 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
operations and financial condition.

The Company also receives royalty revenues which contribute significantly to its
overall profitability. The Company's ability to maintain the anticipated 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 near and long term, the Company expects its
royalty revenue to be affected most significantly by patent expirations. See
"Business - Patents and Other Proprietary Rights" of the Company's Annual Report
on Form 10-K for the fiscal year ended December 31, 1999. In the near term,
Biogen's royalty revenues may also be significantly affected as a result of a
potential dispute with Schering Plough over twelve to eighteen months of
royalties payable by Schering Plough on U.S. sales of INTRON(R) A. As discussed
in the Company's Annual Report on Form 10-K for the fiscal year ended December
31, 1999, a District Court narrowed the scope of Biogen's United States alpha
interferon patent in connection with litigation between Schering Plough,
Biogen's exclusive licensee of the patent, and Amgen Inc. related to alleged
infringement by Amgen of such patent. In the third quarter of 2000, a Court of
Appeals affirmed the District Court's decision. As part of an arbitration with
Biogen related to Schering Plough's REBETRON(R) product, Schering Plough claimed
that as a result of the District Court's decision, it would no longer owe
royalties to Biogen on sales of INTRON(R) A under such patent. As noted in the
Company's Form 10-K for the fiscal year ended December 31, 1999, if Schering
Plough were to pursue this argument and were to be successful, there would be a
twelve to eighteen month gap in royalties from Schering Plough on sales of
INTRON(R) A in the U.S. commencing with product manufactured after the
expiration of Biogen's Irish patent in January 2001.


                                       14
<PAGE>   15
In any event, commencing in July 2002, Schering Plough is obligated to pay
royalties on sales of its alpha interferon products in the U.S., including
INTRON(R) A, during the term of a certain Roche/Genentech U.S. alpha interferon
patent right under an agreement between Biogen and Schering Plough in connection
with settlement of a lawsuit with Roche/Genentech related to the Roche/Genentech
patent right. Biogen is currently in discussions with Schering Plough to
determine Schering Plough's position and to work to resolve the twelve to
eighteen month royalty issue and to resolve claims by Biogen related to
underpayment of royalties by Schering Plough.

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 competition in the MS
market and regulatory matters, see the Company's Annual Report on Form 10-K for
the period ended December 31, 1999 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."

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 continues 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 overcome technical hurdles that may arise, to meet applicable
regulatory standards, 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.


                                       15
<PAGE>   16

PART II - OTHER INFORMATION


Item 3 - Litigation

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 (U.S. Patent No.
5,376,567) in the United States in the production of Biogen's AVONEX(R)
(Interferon beta-la) product. In November 1996, Berlex's New Jersey action was
transferred to the United States District Court in Massachusetts and
consolidated for pre-trial purposes with a related declaratory judgment 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 related to the McCormick patent (U.S. Patent
No. 5,795,779). On September 23, 1998, the cases were consolidated for pre-trial
and trial purposes. Berlex sought a judgment granting it damages, a trebling of
any damages awarded and a permanent injunction restraining Biogen from the
alleged infringement. A hearing on the parties' summary judgment motions in the
case was completed in March 2000. In September 2000, the District Court rendered
final judgement in favor of Biogen and against Berlex determining that Biogen's
production of AVONEX(R) did not infringe any of the claims of the Berlex
patents. Berlex has appealed this decision with the Court of Appeals for the
Federal Circuit. An unfavorable ruling on appeal would result in the case being
remanded to the District Court for trial. If Berlex were to be successful in its
appeal and the case were remanded, an unfavorable ruling in the remanded case
could have a material adverse effect on the Company's results of operations and
financial position. The Company believes that the decision of the District Court
that Biogen does not infringe the Berlex patents is sound, but the ultimate
outcome of the appeal is not currently determinable. As a result, an estimate of
any potential loss or range of loss cannot be made at this time.

Item 6 - Exhibits and Reports on Form 8-K

(a) Exhibits

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


                                       16
<PAGE>   17

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 14, 2000                      /s/ Peter N. Kellogg
                                              ------------------------------
                                              Chief Financial Officer
                                              And Vice President Finance



EXHIBITS
--------

Index to Exhibit.

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

                                       17