<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 JUNE 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 July 20, 2000 was 147,976,357 shares.


                                       1
<PAGE>   2


                                  BIOGEN, INC.

                                      INDEX


<TABLE>
<CAPTION>
PART I - FINANCIAL INFORMATION                                                                                 PAGE NUMBER

<S>                                                                                                            <C>
Condensed Consolidated Statements of Income - Three and six months ended June 30, 2000 and 1999                     3

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

Condensed Consolidated Statements of Cash Flows -
    Six months ended June 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
</TABLE>


 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                      Six Months Ended
                                                             June 30,                               June 30,
                                                      2000               1999               2000               1999
                                                   ---------          ---------           ---------          ---------

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

      Product                                      $ 190,009          $ 145,852           $ 364,605          $ 277,172
      Royalties                                       40,505             43,077              82,757             83,477
                                                   ---------          ---------           ---------          ---------

Total revenues                                       230,514            188,929             447,362            360,649
                                                   ---------          ---------           ---------          ---------

COSTS AND EXPENSES:

      Cost of revenues                                30,795             26,961              59,418             51,831
      Research and development                        71,701             50,941             134,707            101,928
      Selling, general and administrative             40,921             36,999              82,104             70,860
                                                   ---------          ---------           ---------          ---------

Total costs and expenses                             143,417            114,901             276,229            224,619
                                                   ---------          ---------           ---------          ---------

Income from operations                                87,097             74,028             171,133            136,030
Other income, net                                     16,737             (9,270)            115,761             (3,086)
                                                   ---------          ---------           ---------          ---------

INCOME BEFORE INCOME TAXES                           103,834             64,758             286,894            132,944
Income taxes                                          31,774             21,370              93,468             43,872
                                                   ---------          ---------           ---------          ---------

NET INCOME                                         $  72,060          $  43,388           $ 193,426          $  89,072
                                                   =========          =========           =========          =========

BASIC EARNINGS PER SHARE                           $    0.48          $    0.29           $    1.29          $    0.59
                                                   =========          =========           =========          =========
DILUTED EARNINGS PER SHARE                         $    0.47          $    0.28           $    1.24          $    0.57
                                                   =========          =========           =========          =========

SHARES USED IN COMPUTING:
Basic earnings per share                             148,643            150,047             149,501            149,722
                                                   =========          =========           =========          =========
Diluted earnings per share                           154,150            157,575             155,931            157,553
                                                   =========          =========           =========          =========
</TABLE>


            See Notes to Condensed Consolidated Financial Statements.


                                       3
<PAGE>   4


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

<TABLE>
<CAPTION>
                                                        June 30,             December 31,
                                                          2000                   1999
                                                       -----------           ------------
                                                       (unaudited)
<S>                                                    <C>                   <C>
ASSETS
Current assets
       Cash and cash equivalents                       $    67,462           $    56,920
       Marketable securities                               584,725               597,619
       Accounts receivable, net                            154,301               137,363
       Deferred tax assets                                  59,731                50,565
       Other current assets                                 75,613                67,759
                                                       -----------           -----------
       Total current assets                                941,832               910,226
                                                       -----------           -----------

Property, plant and equipment
       Cost                                                427,514               351,566
       Less accumulated depreciation                       124,715               111,789
                                                       -----------           -----------
       Property, plant and equipment, net                  302,799               239,777
                                                       -----------           -----------

Patents, net                                                13,562                13,871
Marketable securities                                       46,422                98,017
Other assets                                                16,646                16,082
                                                       -----------           -----------
                                                       $ 1,321,261           $ 1,277,973
                                                       ===========           ===========

LIABILITIES AND SHAREHOLDERS' EQUITY
Current liabilities
       Accounts payable                                $    23,467           $    30,125
       Current portion of long-term debt                     4,888                 4,888
       Accrued expenses and other                          183,804               155,257
                                                       -----------           -----------
       Total current liabilities                           212,159               190,270
                                                       -----------           -----------

Long-term debt, less current portion                        49,630                52,073
Other long-term liabilities                                 56,279                56,100
Commitments and contingencies                                   --                    --

Shareholders' equity
       Common stock                                          1,514                 1,507
       Additional paid-in capital                          752,747               676,673
       Retained earnings                                   435,481               352,016
       Accumulated other comprehensive income               29,599                45,618
       Treasury stock, at cost                            (216,148)              (96,284)
                                                       -----------           -----------
Total shareholders' equity                               1,003,193               979,530
                                                       -----------           -----------
                                                       $ 1,321,261           $ 1,277,973
                                                       ===========           ===========
</TABLE>


            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>
                                                                                  Six Months Ended
                                                                                      June 30,
                                                                              2000                1999
                                                                            ---------           ---------

<S>                                                                         <C>                 <C>
CASH FLOWS FROM OPERATING ACTIVITIES
      Net income                                                            $ 193,426           $  89,072
      Adjustments to reconcile net income to
         net cash provided from operating activities:
         Depreciation and amortization                                         16,321              15,496
         Deferred income taxes                                                    268               2,119
         Other                                                                  2,697                 379
         Gain on sale of non-current marketable securities                   (101,129)                 --
         Write-down of non-current marketable securities                           --              15,287
         Changes in:
             Accounts receivable                                              (16,938)            (11,887)
             Other current and other assets                                    (2,781)             (7,384)
             Accounts payable, accrued expense and
                other current and long-term liabilities                        22,263             (11,704)
                                                                            ---------           ---------
      Net cash from operating activities                                      114,127              91,378
                                                                            ---------           ---------

CASH FLOWS FROM INVESTING ACTIVITIES
      Purchases of marketable securities                                     (360,510)           (329,515)
      Proceeds from sales and maturities of marketable securities             374,940             258,276
      Proceeds from sales of non-current marketable securities                120,199                  --
      Acquisitions of property and equipment                                  (80,468)            (25,992)
      Additions to patents                                                     (2,182)             (1,605)
                                                                            ---------           ---------
         Net cash from investing activities                                    51,979             (98,836)
                                                                            ---------           ---------

CASH FLOWS FROM FINANCING ACTIVITIES
      Payments of long-term debt                                               (2,443)             (2,444)
      Purchases of treasury stock                                            (250,727)            (68,584)
      Proceeds from put warrants                                                   --               8,332
      Issuance of common stock, stock option exercises and related
         tax benefits                                                          97,606              97,329
                                                                            ---------           ---------
         Net cash from investing activities                                  (155,564)             34,633
                                                                            ---------           ---------

NET INCREASE IN CASH AND CASH EQUIVALENTS                                      10,542              27,175

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

CASH AND CASH EQUIVALENTS, END OF PERIOD                                    $  67,462           $  52,620
                                                                            =========           =========
</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. Certain amounts for the three
and six months ended June 30, 1999 have been reclassified to conform to the
current period presentation.

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>
                                                     June 30,       December 31,
(in thousands)                                         2000             1999
                                                     --------       ------------

<S>                                                  <C>              <C>
Raw materials                                        $ 6,397          $ 5,679
Work in process                                       13,035           15,110
Finished goods                                        20,423           19,242
                                                     -------          -------
                                                     $39,855          $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 June 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 $37.8 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 June 30, 2000, representing the cash the Company would receive to
settle the agreements, was approximately $561,000. The Company has


                                       6
<PAGE>   7


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 six months ended June 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 ninety 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 June 30, 2000 was approximately $127.9 million. These contracts had a fair
value of approximately $10.9 million, representing an unrealized gain, and were
included in other current assets at June 30, 2000.

For the three and six months ended June 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 six months
ended June 30, 2000, approximately $388,000 and $392,000, 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 six months ended June 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 $2.3 million and $4.8 million of
gains in product revenue for the settlement of certain effective cash flow hedge
instruments for the three and six months period ended June 30, 2000,
respectively. The Company recognized $426,000 and $1.1 million of gains in
royalty revenue for the settlement of certain effective cash flow hedge
instruments for the three and six months period ended June 30, 2000,
respectively. For the three and six months ended June 30, 1999, the Company
recognized $1.9 million and $2.8 million of gains in product revenue for the
settlement of certain cash flow hedge instruments, respectively. For the three
and six months ended June 30, 1999, the Company recognized $778,000 and $1.3
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 affecting 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 June 30, 2000 and 1999 was $77.1 million and $58.1 million, respectively.
Comprehensive income for the six months ended June 30, 2000 and 1999 was $177.4
million and $107.2 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 1.7 million shares were outstanding at June 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                Six Months Ended
                                                    June 30,                         June 30,
(in thousands)                               2000             1999             2000             1999
                                            -------          -------          -------          -------

<S>                                         <C>              <C>              <C>              <C>
Weighted average number of shares
      of common stock outstanding           148,643          150,047          149,501          149,722
Dilutive stock options                        5,507            7,528            6,430            7,831
                                            -------          -------          -------          -------
Shares used in calculating diluted
     earnings per share                     154,150          157,575          155,931          157,553
                                            =======          =======          =======          =======
</TABLE>

5. SHARE REPURCHASE PROGRAM

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 six months of 2000, the Company repurchased approximately
3.7 million shares of its common stock at a cost of $250.7 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 1 million were outstanding at June 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 July 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                       Six Months Ended
                                           June 30,                                June 30,
                                 -----------------------------           -----------------------------
                                    2000                1999                2000                1999
                                 ---------           ---------           ---------           ---------
<S>                              <C>                 <C>                 <C>                 <C>
Interest income                  $  10,370           $   8,466           $  21,107           $  16,263
Interest expense                    (1,080)             (1,170)             (2,185)             (2,356)
Other income (expense)               7,447             (16,566)             96,839             (16,993)
                                 ---------           ---------           ---------           ---------

Total other income, net          $  16,737           $  (9,270)          $ 115,761           $  (3,086)
                                 =========           =========           =========           =========
</TABLE>


Other income for the three and six months ended June 30, 2000 includes
non-recurring gains on the sale of certain non-current marketable securities
totaling approximately $8.7 million and $101.1 million, respectively. Other
expense for the three and six months ended June 30, 1999 includes 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
June 30, 2000 and 1999 was approximately 31% and 33%, respectively. Income tax
expense as a percentage of pre-tax income for the six months ended June 30, 2000
and 1999 was approximately 33%, respectively. During the three and


                                       8
<PAGE>   9


six months ended June 30, 2000, the Company recognized non-recurring gains on
the sale of certain non-current marketable securities. Excluding the tax effect
on these non-recurring gains the Company's effective tax rate for the three and
six months ended June 30, 2000 was approximately 30%. The effective tax rate
varied from the U.S. statutory rates for the first six 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 seeks a judgment 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
hearing on the parties' summary judgment motions was completed in March 2000.
Biogen moved for summary judgment of non-infringement of certain claims of the
`567 patent, non-infringement of the `779 patent, as well as a determination of
the invalidity of certain claims of the `567 patent and all of the claims of the
`779 patent. Berlex moved to dismiss Biogen's inequitable conduct defenses and
counterclaims. Berlex also moved for a declaration of literal infringement of
certain claims of the `567 and the `779 patents. No decisions have been rendered
to date. The Company expects a trial to occur in the first half of 2001.

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 has been scheduled for October 2000. 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.


                                       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 June 30, 2000, the Company reported net income of $72.1
million or $0.47 per diluted share as compared to $43.4 million or $0.28 per
diluted share for the comparable period of 1999. For the six months ended June
30, 2000, the Company reported net income of $193.4 million or $1.24 per diluted
share as compared to $89.1 million or $0.57 per diluted share for the comparable
period of 1999.

Total revenues for the quarter ended June 30, 2000 were $230.5 million, as
compared to $188.9 million in the same period of 1999, an increase of $41.6
million or approximately 22%. Total revenues for the six months ended June 30,
2000 were $447.4 million, as compared to $360.6 million in the same period of
1999, an increase of $86.8 million or approximately 24%.

Product revenues in the current quarter were $190 million as compared to $145.9
million for the same period of 1999, an increase of $44.1 million or
approximately 30%. Product revenues in the six months ended June 30, 2000 were
$364.6 million as compared to $277.2 million for the same period of 1999, an
increase of $87.4 million or approximately 32%. Product revenues from AVONEX(R)
represent approximately 82% of the Company's total revenues in the current
quarter and six months ended June 30, 2000 as compared to 77% for the three and
six month periods of 1999. The growth in the three and six month periods ended
June 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 $51.2 million and $99.5 million in the
three and six months ended June 30, 2000 as compared to $42.1 million and $78
million in the same periods of 1999, respectively.

Revenues from royalties in the three months ended June 30, 2000 were $40.5
million, a decrease of $2.6 million or approximately 6% as compared to $43.1
million of royalty revenue for the same period in 1999. Revenues from royalties
in the six months ended June 30, 2000 were $82.8 million, a decrease of
approximately 1% as compared to $83.5 million of royalty revenue for the same
period in 1999. Revenues from royalties represented approximately 18% of total
revenues for the three and six months ended June 30, 2000 as compared to 23% 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). The Company expects to experience declining royalty revenues as a
result of patent expirations. In 2000, the Company expects the decline in
royalty revenues to be partially offset by increasing overall sales of licensed
products. In addition, sales levels of products sold by the Company's licensees
may also fluctuate from quarter to quarter due to the timing and extent of major
events such as new indication approvals or government sponsored programs.


                                       10
<PAGE>   11


COSTS AND EXPENSES

Total costs and expenses for the three months ended June 30, 2000 were $143.4
million as compared to $114.9 million in the same period of 1999, an increase of
approximately 25%. Total costs and expenses for the six months ended June 30,
2000 were $276.2 million as compared to $224.6 million in the same period of
1999, an increase of approximately 23%.

Cost of revenues in the three months ended June 30, 2000 totaled $30.8 million
compared to $27 million in the same period of 1999, an increase of $3.8 million
or 14%. Cost of revenues in the six months ended June 30, 2000 totaled $59.4
million compared to $51.8 million in the same period of 1999, an increase of
$7.6 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 June 30, 2000 and 1999 is $27.5 million and $22.9 million,
respectively, of costs related to product revenues and $3.3 million and $4.1
million, respectively, of costs related to royalty revenue. Included in cost of
revenues for the six months ended June 30, 2000 and 1999 is $53.5 million and
$44.2 million, respectively, of costs related to product revenues and $5.9
million and $7.6 million, respectively, of costs related to royalty revenue.
Gross margins on product revenues increased to approximately 86% for the three
months ended June 30, 2000 compared to 84% in the same period in 1999. Gross
margins on product revenues increased to approximately 85% for the six months
ended June 30, 2000 compared to 84% in the same period in 1999. Gross margins on
royalty revenue increased to approximately 92% for the three months ended June
30, 2000 compared to 90% in the same period in 1999. Gross margins on royalty
revenue increased to approximately 93% for the six months ended June 30, 2000
compared to 91% 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 $71.7 million, an
increase of $20.8 million or 41% as compared to $50.9 million in the same period
of 1999. Research and development expenses in the six months ended June 30, 2000
were $134.7 million, an increase of $32.8 million or 32% as compared to $101.9
million in the same period of 1999. The increase was primarily due to 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).

Selling, general and administrative expenses in the second quarter of 2000 were
$40.9 million, an increase of $3.9 million or 11% as compared to the same period
of 1999. Selling, general and administrative expenses in the six months ended
June 30, 2000 were $82.1 million, an increase of $11.2 million or 16% 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 current quarter of 2000 was $16.7 million as compared to other expense,
net of $9.3 million in 1999, an increase of $26 million. Other income, net in
the six months ended June 30, 2000 was $115.8 million as compared to other
expense, net of $3.1 million in 1999, an increase of $118.9 million. Interest
income for the three months ended June 30, 2000 was $10.4 million compared to
$8.5 million in the same period of 1999, an increase of $1.9 million or 22%.
Interest income for the six months ended June 30, 2000 was $21.1 million
compared to $16.3 million in the same period of 1999, an increase of $4.8
million or 29%. The increase in interest income for the three and six months
ended June 30, 2000 is due primarily to an increase in funds invested. In the
three months ended June 30, 2000 interest expense decreased to $1.1 million from
$1.2 million compared to the same period in 1999. In the six months ended June
30, 2000 interest expense decreased to $2.2 million from $2.4 million


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<PAGE>   12


compared to the same period in 1999. Other non-operating income (expense)
increased by $24 million in the three months ended June 30, 2000 from the same
period in 1999. Other non-operating income (expense) increased by $113.8 million
in the six months ended June 30, 2000 from the same period in 1999. The increase
in non-operating income is due primarily to the sale of certain non-current
marketable securities generating non-recurring gains of approximately $8.7
million and $101.1 million in the three and six months ended June 30, 2000.
Additionally, other expense in the three and six months ended June 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
June 30, 2000 and 1999 was approximately 31% and 33%, respectively. Income tax
expense as a percentage of pre-tax income for the six months ended June 30, 2000
and 1999 was approximately 33%, respectively. During the three and six months
ended June 30, 2000, the Company recognized non-recurring gains on the sale of
certain non-current marketable securities. Excluding the tax effect on these
non-recurring gains the Company's effective tax rate for the three and six
months ended June 30, 2000 was approximately 30%. The effective tax rate varied
from the U.S. statutory rates for the first six 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 June 30, 2000, cash, cash equivalents and short-term marketable securities
were $652.2 million compared with $654.5 million at December 31, 1999, a
decrease of $2.3 million. Working capital increased $9.7 million to $729.7
million. Net cash from operating activities for the period ended June 30, 2000
was $114.1 million compared with $91.4 million for the same period in 1999.
Significant cash inflows from investing activities during the first six months
of 2000 included $120.2 million in proceeds from the sale of certain non-current
marketable securities. Cash outflows during the first six months of 2000
included investments in property and equipment and patents of $82.7 million.
Significant cash outflows from financing activities included $250.7 million for
purchases of the Company's common stock under its stock repurchase program and
$2.4 million for repayments on loan agreements with banks. Cash inflows included
$97.6 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 six months of 2000, the Company repurchased approximately
3.7 million shares of its common stock at a cost of $250.7 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 1 million were outstanding at June 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 July 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


                                       12
<PAGE>   13


of 2001 at a total cost of approximately $95 million, of which $78 million had
been committed at June 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 $114 million had been committed at June
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. 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, 1999 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 raise additional capital to
take advantage of favorable conditions in the market or in connection with the
Company's development activities.

NEW ACCOUNTING PRONOUNCEMENTS

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.

In March 2000, the Financial Accounting Standard Board issued FASB
Interpretation No. 44, "Accounting for Certain Transactions Involving Stock
Compensation - an interpretation of APB Opinion No. 25" ("FIN 44"). FIN 44
clarifies the application of APB Opinion No. 25 and among other issues clarifies
the following: the definition of an employee for purposes of applying APB
Opinion No. 25; the criteria for determining whether a plan qualifies as a
noncompensatory plan; the accounting consequence of various modifications to the
terms of previously fixed stock options or awards; and the accounting for an
exchange of stock compensation awards in a business combination. FIN 44 is
effective July 1, 2000, but certain conclusions in FIN 44 cover specific events
that occurred after either December 15, 1998 or January 12, 2000. The Company
does not expect the application of FIN 44 to have a material impact on the
Company's financial position or results of operations.


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.


                                       13
<PAGE>   14


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 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 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. The Company's
royalty revenue could also be negatively affected if there is an adverse
decision in the appeal of a claim interpretation narrowing the scope of Biogen's
alpha interferon patent. The appeal is part of an action between Schering-Plough
Corporation and Amgen, Inc. but relates to Biogen's patent. 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 and the Amgen appeal, 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


                                       14
<PAGE>   15


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 4 - Submission of Matters to a Vote of Security Holders

(a)  The information set forth in this Item 4 relates to matters submitted to a
     vote at the Annual Meeting of Stockholders of Biogen, Inc. on June 16,
     2000.

(b)  Not applicable.

(c)  A proposal to elect Harold W. Buirkle, Alan K. Simpson and James L. Vincent
     as directors to serve for a three year term ending in 2003 and until their
     successors are duly elected and qualified was approved with the following
     vote:

          Nominee                       For                 Abstains
          -------                       ---                 --------
     Harold W. Buirkle              116,423,421             991,570
     Alan K. Simpson                116,430,206             984,785
     James L. Vincent               116,438,117             976,874

     A proposal to ratify the selection of PricewaterhouseCoopers LLP as the
     Company's independent accountants for the fiscal year ending December 31,
     2000 was approved with 116,894,929 affirmative votes, 122,085 negative
     votes, 397,340 abstentions and 637 broker non-votes.

(d)  Not applicable.

Item 5 - Other Information

On July 10, 2000, the Company announced that Peter N. Kellogg had been appointed
Vice President, Finance and Chief Financial Officer, effective August 7, 2000.

Item 6 - Exhibits and Reports on Form 8-K


(a) Exhibits

No. 10.1     1982 Incentive Stock Option Plan (as amended through
             June 15, 2000).

No. 10.2     1985 Non-Qualified Stock Option Plan (as amended through
             June 15, 2000).

No. 10.3     1987 Scientific Board Stock Option Plan (as amended through
             June 15, 2000).

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: August 3, 2000                     /s/ Michael A. Kelly
                                          --------------------------------------

                                          Corporate Controller and
                                          Acting Chief Financial Officer



EXHIBITS

Index to Exhibit.

No. 10.1     1982 Incentive Stock Option Plan (as amended through
             June 15, 2000).

No. 10.2     1985 Non-Qualified Stock Option Plan (as amended through
             June 15, 2000).

No. 10.3     1987 Scientific Board Stock Option Plan (as amended through
             June 15, 2000).

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



                                       17