<PAGE>
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                                 UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION

                             WASHINGTON, D.C. 20549

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

                                  FORM 10-Q/A

<TABLE>
<C>        <S>
   /X/     QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
           SECURITIES EXCHANGE ACT OF 1934
</TABLE>

                 FOR THE QUARTERLY PERIOD ENDED MARCH 31, 2000
                                       OR

<TABLE>
<C>        <S>
   / /     TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
           SECURITIES EXCHANGE ACT OF 1934
</TABLE>

        FOR THE TRANSITION PERIOD FROM ______________ TO ______________

                         COMMISSION FILE NUMBER 0-27628

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

                                 SUPERGEN, INC.

             (Exact name of registrant as specified in its charter)

<TABLE>
<S>                                            <C>
               DELAWARE                                     91-1841574
     (State or other jurisdiction              (IRS Employer Identification Number)
   of incorporation or organization)

     TWO ANNABEL LANE, SUITE 220,                             94583
         SAN RAMON, CALIFORNIA                              (Zip Code)
    (Address of principal executive
               offices)
</TABLE>

                                 (925) 327-0200
              (Registrant's telephone number, including area code)

                                 NOT APPLICABLE
   (Former name, former address and former fiscal year, if changed since last
                                    report)

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

    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 / /

                      APPLICABLE ONLY TO CORPORATE ISSUERS

    The number of shares of the registrant's Common Stock, $.001 par value,
outstanding as of May 10, 2000, was 32,656,939.

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<PAGE>
                               TABLE OF CONTENTS

<TABLE>
<CAPTION>
                                                                                  PAGE
                                                                                  NO.
                                                                                --------
<S>      <C>      <C>                                                           <C>
PART I            FINANCIAL INFORMATION

         Item 1-- Financial Statements (Unaudited)

                  Consolidated Balance Sheets as of March 31, 2000 and
                    December 31, 1999.........................................         3

                  Consolidated Statements of Operations for the three month
                    periods ended March 31, 2000 and 1999.....................         4

                  Consolidated Statements of Cash Flows for the three month
                    periods ended March 31, 2000 and 1999.....................         5

                  Notes to Consolidated Financial Statements..................         6

         Item 2-- Management's Discussion and Analysis of Financial Condition
                    and Results of Operations.................................        10

         Item 3-- Quantitative and Qualitative Disclosures of Market Risk.....        16

PART II           OTHER INFORMATION

         Item 2-- Changes in Securities and Use of Proceeds...................        17

         Item 6-- Exhibits and Reports on Form 8-K............................        18

SIGNATURES....................................................................        19
</TABLE>

                                       2
<PAGE>
                                 SUPERGEN, INC.

                          CONSOLIDATED BALANCE SHEETS

               (IN THOUSANDS, EXCEPT SHARE AND PER SHARE AMOUNTS)

<TABLE>
<CAPTION>
                                                               MARCH 31,    DECEMBER 31,
                                                                 2000           1999
                                                              -----------   ------------
                                                              (UNAUDITED)     (NOTE 1)
<S>                                                           <C>           <C>
                                         ASSETS

Current assets:
  Cash and cash equivalents.................................   $ 119,530      $ 22,546
  Marketable securities.....................................      10,770         5,008
  Accounts receivable, net..................................       1,105         1,754
  Other receivables.........................................          --         5,000
  Inventories...............................................       1,434         1,368
  Prepaid expenses and other current assets.................       3,323         2,879
                                                               ---------      --------
    Total current assets....................................     136,162        38,555

Property, plant and equipment, net..........................       3,454         2,923
Developed technology at cost, net...........................       1,674         1,707
Goodwill and other intangibles, net.........................       1,911         2,036
Investment in stock of related parties......................      13,000         5,938
Due from related party......................................          --           450
Marketable securities--non-current..........................      10,200         1,812
Other assets................................................          59            57
                                                               ---------      --------
    Total assets............................................   $ 166,460      $ 53,478
                                                               =========      ========

                          LIABILITIES AND STOCKHOLDERS' EQUITY

Current liabilities:
  Accounts payable and accrued liabilities..................   $   3,100      $  2,694
  Deferred revenue..........................................       1,000           894
  Accrued employee benefits.................................         838           955
                                                               ---------      --------
    Total current liabilities...............................       4,938         4,543

Deferred revenue--non-current...............................       3,917         4,167
                                                               ---------      --------
    Total liabilities.......................................       8,855         8,710
                                                               ---------      --------
Stockholders' equity:
  Preferred stock, $.001 par value; 2,000,000 shares
    authorized; none outstanding............................          --            --
  Common stock, $.001 par value; 40,000,000 shares
    authorized; 30,555,785 and 25,477,770 shares issued and
    outstanding at March 31, 2000 and December 31, 1999,
    respectively............................................          31            25
  Additional paid in capital................................     251,509       138,461
  Deferred compensation.....................................        (777)         (835)
  Accumulated other comprehensive gain (loss)...............       7,259            (5)
  Accumulated deficit.......................................    (100,417)      (92,878)
                                                               ---------      --------
    Total stockholders' equity..............................     157,605        44,768
                                                               ---------      --------
    Total liabilities and stockholders' equity..............   $ 166,460      $ 53,478
                                                               =========      ========
</TABLE>

          See accompanying notes to consolidated financial statements

                                       3
<PAGE>
                                 SUPERGEN, INC.

                     CONSOLIDATED STATEMENTS OF OPERATIONS

                    (IN THOUSANDS, EXCEPT PER SHARE AMOUNTS)

                                  (UNAUDITED)

<TABLE>
<CAPTION>
                                                              THREE MONTHS ENDED
                                                                   MARCH 31,
                                                              -------------------
                                                                2000       1999
                                                              --------   --------
<S>                                                           <C>        <C>
Revenues:
  Net sales revenue.........................................  $   695    $   916
  Other revenue.............................................      144         --
                                                              -------    -------
    Total revenue...........................................      839        916

Operating expenses:
  Cost of sales.............................................      124        708
  Research and development..................................    6,347      3,120
  Selling, general, and administrative......................    2,936      2,095
                                                              -------    -------
    Total operating expenses................................    9,407      5,923
                                                              -------    -------
Loss from operations........................................   (8,568)    (5,007)

Interest income.............................................    1,029        140
                                                              -------    -------
Net loss....................................................  $(7,539)   $(4,867)
                                                              =======    =======
Basic net loss per share....................................  $ (0.27)   $ (0.23)
                                                              =======    =======
Weighted average shares used in basic net loss per share
  calculation...............................................   27,912     21,063
                                                              =======    =======
</TABLE>

          See accompanying notes to consolidated financial statements

                                       4
<PAGE>
                                 SUPERGEN, INC.

                     CONSOLIDATED STATEMENTS OF CASH FLOWS

                                 (IN THOUSANDS)

                                  (UNAUDITED)

<TABLE>
<CAPTION>
                                                              THREE MONTHS ENDED
                                                                   MARCH 31,
                                                              -------------------
                                                                2000       1999
                                                              --------   --------
<S>                                                           <C>        <C>
Operating activities:
  Net loss..................................................  $ (7,539)  $(4,867)
  Adjustments to reconcile net loss to net cash used in
    operating activities:
    Depreciation and amortization...........................       351       185
    Expense related to stock options and warrants granted to
      non-employees.........................................        --        43
    Amortization of deferred revenue........................      (144)       --
    Changes in operating assets and liabilities:
      Accounts receivable...................................       649      (164)
      Inventories...........................................       (66)       96
      Prepaid expenses and other assets.....................      (446)   (1,312)
      Other receivables.....................................     5,000        --
      Accounts payable and other liabilities................       289       803
      Due from related parties..............................        --       (10)
                                                              --------   -------
Net cash used in operating activities.......................    (1,906)   (5,226)
Investing activities:
  Purchases of marketable securities........................   (13,807)       --
  Sales or maturities of marketable securities..............      (141)    2,035
  Purchase of property and equipment........................      (216)      (35)
                                                              --------   -------
Net cash provided by (used in) investing activities:........   (14,164)    2,000
Financing activities:
  Issuance of common stock, net of issuance costs...........   113,054       362
                                                              --------   -------
Net cash provided by financing activities...................   113,054       362
                                                              --------   -------
Net increase (decrease) in cash and cash equivalents........    96,984    (2,864)
Cash and cash equivalents at beginning of period............    22,546     8,614
                                                              --------   -------
Cash and cash equivalents at end of period..................  $119,530   $ 5,750
                                                              ========   =======
</TABLE>

          See accompanying notes to consolidated financial statements

                                       5
<PAGE>
                                 SUPERGEN, INC.

                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS

                                 MARCH 31, 2000

                                  (UNAUDITED)

NOTE 1.  BASIS OF PRESENTATION

    The accompanying unaudited consolidated financial statements of
SuperGen, Inc. ("we," "SuperGen" or "the Company") have been prepared in
accordance with generally accepted accounting principles for interim financial
information on a basis consistent with the audited financial statements for the
year ended December 31, 1999 and in accordance with the instructions to
Form 10-Q. The consolidated financial statements include the accounts of Sparta
Pharmaceuticals, Inc. and two other wholly owned subsidiaries, which are
immaterial. The statements include all adjustments (consisting of normal
recurring accruals) which in our opinion are necessary for a fair presentation
of the results for the periods presented. The interim results are not
necessarily indicative of results that may be expected for the full year.

    The balance sheet at December 31, 1999 has been derived from the audited
financial statements at that date but does not include all the information and
footnotes required by generally accepted accounting principles for complete
financial statements.

    For further information, refer to the consolidated financial statements and
footnotes included in the Company's annual report on Form 10-K for the year
ended December 31, 1999.

    We have reclassified certain prior year amounts to conform to the current
year's presentation.

NOTE 2.  CASH, CASH EQUIVALENTS, AND MARKETABLE SECURITIES

    Cash and cash equivalents include bank demand deposits, certificates of
deposit, investments in debt securities with maturities of three months or less
when purchased, and an interest in money market funds which invest primarily in
U.S. government obligations and commercial paper. These instruments are highly
liquid and are subject to insignificant risk.

    Investments in marketable securities consist of corporate or government debt
securities that have a readily ascertainable market value and are readily
marketable. We report these investments at fair value. We designate all debt
securities as available-for-sale, with unrealized gains and losses included in
equity.

    The following is a summary of available-for-sale securities as of March 31,
2000 (in thousands):

<TABLE>
<CAPTION>
                                                             GROSS
                                             AMORTIZED     UNREALIZED     ESTIMATED
                                               COST      GAINS (LOSSES)   FAIR VALUE
                                             ---------   --------------   ----------
<S>                                          <C>         <C>              <C>
U.S. corporate debt securities.............  $120,551        $  (83)       $120,468
Marketable equity securities...............     5,492         7,342          12,834
                                             --------        ------        --------
  Total....................................  $126,043        $7,259        $133,302
                                             ========        ======        ========
</TABLE>

                                       6
<PAGE>
                                 SUPERGEN, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

                                 MARCH 31, 2000

                                  (UNAUDITED)

NOTE 2.  CASH, CASH EQUIVALENTS, AND MARKETABLE SECURITIES (CONTINUED)
    Balance sheet classification as of March 31, 2000 (in thousands):

<TABLE>
<CAPTION>
                                                             GROSS
                                             AMORTIZED     UNREALIZED     ESTIMATED
                                               COST      GAINS (LOSSES)   FAIR VALUE
                                             ---------   --------------   ----------
<S>                                          <C>         <C>              <C>
Cash and cash equivalents..................  $ 99,851        $  (19)       $ 99,832
Marketable securities, current.............    10,800           (30)         10,770
Marketable securities, non-current.........    10,067           133          10,200
Investment in stock of related party.......     5,325         7,175          12,500
                                             --------        ------        --------
  Total....................................  $126,043        $7,259        $133,302
                                             ========        ======        ========
</TABLE>

    Available-for-sale securities by contractual maturity (in thousands):

<TABLE>
<CAPTION>
                                                        MARCH 31,    DECEMBER 31,
                                                           2000          1999
                                                        ----------   -------------
<S>                                                     <C>          <C>
Debt securities:
Due in one year or less...............................   $110,602       $22,846
Due after one year through three years................      9,866         1,753
                                                         --------       -------
                                                          120,468        24,599
Marketable equity securities..........................     12,834         5,497
                                                         --------       -------
  Total...............................................   $133,302       $30,096
                                                         ========       =======
</TABLE>

    There were no realized gains and losses for the three months ended
March 31, 2000 and 1999.

NOTE 3.  INVENTORIES

    Inventories consist of the following (in thousands):

<TABLE>
<CAPTION>
                                                        MARCH 31,   DECEMBER 31,
                                                          2000          1999
                                                        ---------   ------------
<S>                                                     <C>         <C>
Raw material..........................................   $  183        $  183
Work in process.......................................    1,086           935
Finished goods........................................      165           250
                                                         ------        ------
                                                         $1,434        $1,368
                                                         ======        ======
</TABLE>

NOTE 4.  STOCKHOLDERS' EQUITY

FOLLOW-ON OFFERING OF COMMON STOCK

    In March 2000, we concluded a public follow-on offering of our common stock.
We issued 1,465,000 shares of registered stock, resulting in net proceeds to the
Company of approximately $61,000,000.

                                       7
<PAGE>
                                 SUPERGEN, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

                                 MARCH 31, 2000

                                  (UNAUDITED)

NOTE 4.  STOCKHOLDERS' EQUITY (CONTINUED)
PUBLIC WARRANTS

    On September 20, 1999, we issued a notice that we would redeem our 1996
publicly traded $9.00 warrants ("SUPGW" warrants) outstanding at April 16, 2000
at $0.25 per warrant. During the quarter ended March 31, 2000, 1,623,000 of the
SUPGW warrants were exercised, resulting in proceeds to the Company of
approximately $14,600,000. Also during the quarter, we received an additional
$4,500,000 upon exercise of underwriters' warrants that had been issued in
connection with our initial public offering.

    Subsequent to March 31, 2000, an additional 2,094,000 SUPGW warrants were
exercised, resulting in proceeds of approximately $18,850,000. At April 16,
2000, over 99.9% of the outstanding SUPGW warrants had been exercised.

NOTE 5.  AGREEEMENTS WITH ABBOTT LABORATORIES

    In December 1999, we entered into agreements with Abbott Laboratories
("Abbott") under which Abbott will undertake to market and distribute our
products, and invest in shares of our common stock. In January 2000, Abbott made
a $26.5 million equity investment in the Company as part of the agreement
covering the development, marketing, and distribution of rubitecan.

    Under the terms of the Nipent distribution agreement, beginning March 1,
2000, Abbott became the exclusive U.S. distributor of Nipent for a period of
five years. We retain U.S. marketing rights for Nipent. In accordance with this
agreement, in January 2000, Abbott made a $5 million cash payment to the
Company. This amount is being recognized as other revenue ratably over the term
of the agreement and the remaining balance is included in current and
non-current deferred revenue at March 31, 2000.

NOTE 6.  RELATED PARTY TRANSACTIONS--AVI BIOPHARMA, INC.

    In December 1999, we entered into an agreement with AVI BioPharma, Inc.
("AVI"). The president of AVI is a member of our Board of Directors. The
president and chief executive officer of SuperGen is a member of the Board of
Directors of AVI. Under the terms of the agreement, we acquired one million
shares of AVI common stock, which amounted to approximately seven and one half
percent (7.5%) of AVI's outstanding common stock, for $2.5 million cash and
100,000 shares of our common stock at $28.25 per share. We also acquired
exclusive negotiating rights for the United States market for Avicine, AVI's
proprietary cancer vaccine currently in late-stage clinical testing against a
variety of solid tumors.

    In April 2000, we completed our negotiations with AVI and entered into an
agreement, subject to regulatory approval, for the U.S. marketing rights for
Avicine in exchange for a $20 million equity investment in shares of AVI common
stock. We will issue approximately 350,000 shares of our common stock along with
$5 million in cash to AVI as payment for our investment, in exchange for
approximately 1.7 million shares of AVI common stock. As part of this agreement,
we obtained the right of first discussion to all of AVI's oncology compounds and
an option to acquire an additional 10% of

                                       8
<PAGE>
                                 SUPERGEN, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

                                 MARCH 31, 2000

                                  (UNAUDITED)

NOTE 6.  RELATED PARTY TRANSACTIONS--AVI BIOPHARMA, INC. (CONTINUED)
AVI's common stock for $35.625 per share. This option is exercisable for a
three-year period commencing on the earlier of the date the Food and Drug
Administration accepts the NDA submitted for Avicine or the date on which the
closing price of AVI's common stock exceeds the option exercise price. We will
account for the investment in AVI under the cost method.

NOTE 7.  COMPREHENSIVE LOSS

    For the three months ended March 31, 2000 and 1999, total comprehensive
losses amounted to $202,000 and $4,828,000, respectively. Comprehensive losses
consisted primarily of the net losses and unrealized gains or losses on
investments.

NOTE 8.  BASIC NET LOSS PER SHARE

    Basic and diluted net loss per common share is computed by dividing net loss
by the weighted average number of shares outstanding during the quarter.

    As we have reported operating losses each period since our inception, the
effect of assuming the exercise of options and warrants would be anti-dilutive
and, therefore, basic and diluted loss per share are the same.

                                       9
<PAGE>
ITEM 2.

                    MANAGEMENT'S DISCUSSION AND ANALYSIS OF
                 FINANCIAL CONDITION AND RESULTS OF OPERATIONS

    YOU SHOULD READ THE FOLLOWING DISCUSSION TOGETHER WITH OUR CONSOLIDATED
FINANCIAL STATEMENTS AND RELATED NOTES INCLUDED ELSEWHERE IN THIS REPORT. THE
RESULTS DISCUSSED BELOW ARE NOT NECESSARILY INDICATIVE OF THE RESULTS TO BE
EXPECTED IN ANY FUTURE PERIODS. TO THE EXTENT THAT THE INFORMATION PRESENTED IN
THIS DISCUSSION ADDRESSES FINANCIAL PROJECTIONS, INFORMATION OR EXPECTATIONS
ABOUT OUR PRODUCTS OR MARKETS OR OTHERWISE MAKES STATEMENTS ABOUT FUTURE EVENTS,
SUCH STATEMENTS ARE FORWARD-LOOKING AND ARE SUBJECT TO A NUMBER OF RISKS AND
UNCERTAINTIES THAT COULD CAUSE ACTUAL RESULTS TO DIFFER MATERIALLY FROM THE
STATEMENTS MADE.

OVERVIEW

    Since our incorporation in 1991 we have devoted substantially all of our
resources to our product development efforts. Our product revenues to date have
been limited and have been principally from sales of Nipent, which we are
marketing in the United States for the treatment of hairy cell leukemia. As a
result of our substantial research and development expenditures and minimal
product revenues, we have incurred cumulative losses of $100.4 million for the
period from inception through March 31, 2000. These losses included non-cash
charges of $18.4 million for the acquisition of in-process research and
development.

    During the first quarter of 2000, we significantly increased our cash and
marketable securities to in excess of $140 million at March 31, 2000. We raised
approximately $61 million through a public offering of our common stock, over
$31 million pursuant to our corporate partnering transactions with Abbott
Laboratories, and received approximately $19 million through the exercise of our
publicly traded warrants issued at the time of our initial public offering
("SUPGW" warrants) and the related underwriters unit purchase warrants.
Subsequent to March 31, 2000, we received an additional $19 million in warrant
exercises in advance of the SUPGW warrant redemption date of April 16, 2000.

    We seek to minimize the time, expense and technical risk associated with
drug commercialization by identifying and acquiring or licensing pharmaceutical
compounds in the later stages of development, rather than committing significant
resources to the research phase of drug discovery. Recently, we completed our
negotiations with AVI BioPharma, Inc. ("AVI") and entered into an agreement,
subject to regulatory approval, for the U.S. marketing rights for Avicine, AVI's
therapeutic cancer vaccine currently in late-stage clinical development for a
variety of solid tumors.

    We will share U.S. developmental and regulatory approval costs for Avicine
and upon commercialization in the U.S. we will split all U.S. profits. AVI and
SuperGen will jointly determine the optimum development strategy for the
international marketplace and will share all profits received. In addition to an
up front equity investment, we will be obligated to make additional payments to
AVI based on successful achievement of developmental, regulatory approval, and
commercialization milestones over the next several years. As part of this
agreement, we obtained the right of first discussion to all of AVI's oncology
compounds and an option to acquire an additional 10% of AVI's common stock.
Avicine will require significant additional expenditures to complete the
clinical development necessary to gain marketing approval from the FDA and
equivalent foreign regulatory agencies.

    We are pursuing the clinical and regulatory development of our other product
candidates internally and expect to continue to incur operating losses at least
through 2000 and into 2001. This is due primarily to projected increases in our
spending for the development of our product candidates, especially rubitecan,
which is in pivotal Phase III clinical trials. Our ability to become profitable
will depend upon a variety of factors, including regulatory approvals of our
products, the timing of the introduction and market acceptance of our products
and competing products, increases in sales and marketing expenses related to the
launch of rubitecan, and our ability to control our costs.

                                       10
<PAGE>
    As part of our strategy, we intend either to market our products ourselves
or co-promote these products with partners. In 1999, we entered into an alliance
with Abbott under which Abbott will undertake to market and distribute
rubitecan. We will co-promote rubitecan with Abbott in the United States and
Abbott has exclusive rights to market rubitecan outside of the United States. In
the U.S. market, we will share profits from product sales equally with Abbott.
Outside the U.S. market, Abbott will pay us royalties and transfer fees based on
product sales. We will remain responsible for pursuing and funding the clinical
development of rubitecan and obtaining regulatory approval for the product in
the United States, Canada and the member states of the European Union.

RESULTS OF OPERATIONS

    THREE MONTHS ENDED MARCH 31, 2000 COMPARED TO THREE MONTHS ENDED MARCH 31,
     1999.

    Revenues were $839,000 in the first quarter of 2000 compared to $916,000 in
the first quarter of 1999. Revenues in the first quarter of 1999 included
approximately $475,000 in sales to the European distributor for Nipent, whereas
revenues from the sale of Nipent in the first quarter of 2000 were comprised
exclusively of U.S. sales. Unlike our Nipent sales efforts in the U.S. market
where we call on clinicians directly, our role in Europe is currently limited to
that of a supplier. As such, we do not have a direct influence on Nipent sales
at the clinical level, making their timing and magnitude difficult to predict
and dependent on the efforts of our European distributor. Based on this existing
relationship, it is our expectation that current inventory levels at our
distributor in Europe will likely result in lower order requirements over the
next several quarters. The first quarter of 2000 also included recognition of
$50,000 in revenue associated with the completion of a clinical trial for
busulfan in Europe and recognition of $83,000 in revenues related to the Nipent
distribution arrangement with Abbott Laboratories.

    Cost of sales as a percentage of net sales revenues was 18% in 2000 compared
to 77% in 1999. The improvement in cost of sales percentage was due primarily to
the absence in 2000 of sales to the European distributor for Nipent, as such
sales were made at a lower unit selling price under a supply agreement for sale
outside North America. Current margins may not be indicative of future margins
due to possible variations in average selling prices and manufacturing costs.

    Research and development expenses were $6,347,000 in 2000 compared to
$3,120,000 in 1999. The increased expense was due primarily to a broader
clinical development program along with its associated costs together with
expansion of the research and development staff.

    Selling, general and administrative expenses were $2,936,000 in 2000
compared to $2,095,000 in 1999. This increase was due primarily to costs
associated with the expansion of the sales, professional services and general
and administrative staffs. Additionally, legal expenses associated with both
corporate and patent matters increased over 1999 levels.

    Interest income was $1,029,000 in the first quarter of 2000 compared to
$140,000 in the first quarter of 1999. This was due to the greater cash balances
available for investment as a result of our Abbott corporate partnership, the
follow-on offering of our common stock, and the exercise of our SUPGW warrants
and related underwriters' unit purchase warrants.

LIQUIDITY AND CAPITAL RESOURCES

    Our cash, cash equivalents and both short and long term marketable
securities totaled approximately $140 million at March 31, 2000, compared to
approximately $29 million at December 31, 1999. In January 2000, we received a
$26.5 million equity investment and a $5 million cash payment from Abbott.
During the first quarter, we raised approximately $61 million through a
follow-on offering of our common stock and we received approximately
$19 million through the exercise of our SUPGW warrants and related underwriters'
unit purchase warrants.

                                       11
<PAGE>
    The net cash used in operating activities of $1.9 million in the first
quarter primarily reflected the net loss for the period of $7.5 million, offset
by the receipt of $5.0 million from Abbott Laboratories relating to the Nipent
distribution agreement.

    We believe that our current cash, cash equivalents and marketable securities
will satisfy our cash requirements at least through December 31, 2002. Our
primary planned uses of cash during that period are:

    - for research and development activities, including expansion of clinical
      trials;

    - to enhance sales and marketing efforts in advance of the potential launch
      of rubitecan;

    - to lease and improve new facilities and potentially enhance manufacturing
      capabilities; and

    - to finance possible acquisitions of complimentary products, technologies
      and businesses.

    We believe that our need for additional funding will increase in the future
and that our continued ability to raise additional funds from external sources
will be critical to our success. We continue to actively consider future
contractual arrangements that would require significant financial commitments.
If we experience currently unanticipated cash requirements, we could require
additional capital much sooner than presently anticipated. We may seek such
additional funding through public or private financings or collaborative or
other arrangements with third parties. We may not be able to obtain additional
funds on acceptable terms, if at all.

FACTORS AFFECTING FUTURE OPERATING RESULTS

    YOU SHOULD CAREFULLY CONSIDER THE RISKS DESCRIBED BELOW BEFORE MAKING AN
INVESTMENT DECISION. THE RISKS AND UNCERTAINTIES DESCRIBED BELOW ARE NOT THE
ONLY ONES FACING OUR COMPANY. OUR BUSINESS OPERATIONS MAY BE IMPAIRED BY
ADDITIONAL RISKS AND UNCERTAINTIES THAT WE DO NOT KNOW OF OR THAT WE CURRENTLY
CONSIDER IMMATERIAL.

    OUR BUSINESS, RESULTS OF OPERATIONS OR CASH FLOWS MAY BE ADVERSELY AFFECTED
IF ANY OF THE FOLLOWING RISKS ACTUALLY OCCUR. IN SUCH CASE, THE TRADING PRICE OF
OUR COMMON STOCK COULD DECLINE, AND YOU MAY LOSE ALL OR PART OF YOUR INVESTMENT.

    THIS REPORT ALSO CONTAINS AND INCORPORATES BY REFERENCE FORWARD-LOOKING
STATEMENTS THAT INVOLVE RISKS AND UNCERTAINTIES. OUR ACTUAL RESULTS COULD DIFFER
MATERIALLY FROM THOSE ANTICIPATED IN THE FORWARD-LOOKING STATEMENTS AS A RESULT
OF CERTAIN FACTORS, INCLUDING THE RISKS DESCRIBED BELOW AND ELSEWHERE IN THIS
REPORT.

    IF THE RESULTS OF FURTHER CLINICAL TESTING INDICATE THAT OUR PROPOSED
PRODUCTS ARE NOT SAFE AND EFFECTIVE FOR HUMAN USE, OUR BUSINESS WILL SUFFER.
Most of our products are in the development stage and prior to their sale will
require the commitment of substantial resources. All of the potential
proprietary products that we are currently developing will require extensive
preclinical and clinical testing before we can submit any application for
regulatory approval. Before obtaining regulatory approvals for the commercial
sale of any of our products, we must demonstrate through pre-clinical testing
and clinical trials that our product candidates are safe and effective in
humans. Conducting clinical trials is a lengthy, expensive and uncertain
process. Completion of clinical trials may take several years or more. The
length of time generally varies substantially according to the type, complexity,
novelty and intended use of the product candidate. Our clinical trials may be
suspended at any time if we or the FDA believe the patients participating in our
studies are exposed to unacceptable health risks. We may encounter problems in
our studies which will cause us or the FDA to delay or suspend the studies. Our
commencement and rate of completion of clinical trials may be delayed by many
factors, including:

    - ineffectiveness of the study compound, or perceptions by physicians that
      the compound is not effective for a particular indication;

    - inability to manufacture sufficient quantities of compounds for use in
      clinical trials;

                                       12
<PAGE>
    - failure of the FDA to approve our clinical trial protocols;

    - slower than expected rate of patient recruitment;

    - inability to adequately follow patients after treatment;

    - unforeseen safety issues;

    - lack of efficacy during the clinical trials; or

    - government or regulatory delays.

    The clinical results we have obtained to date do not necessarily predict
that the results of further testing, including later-stage controlled human
clinical testing, will be successful. If our trials are not successful, or are
perceived as not successful by the FDA or physicians, our business, financial
condition and results of operations will be harmed.

    IF WE FAIL TO OBTAIN REGULATORY MARKETING APPROVALS IN A TIMELY MANNER, OUR
BUSINESS WILL SUFFER. Even if we believe our trials are successful, the FDA may
require additional clinical testing and, therefore we would have to commit
additional unanticipated resources. The FDA has substantial discretion in the
drug approval process. We cannot assure you that we will obtain the necessary
regulatory approvals to market our products. The FDA and comparable agencies in
foreign countries impose substantial requirements for the introduction of both
new pharmaceutical products and generic products through lengthy and detailed
clinical testing procedures, sampling activities and other costly and
time-consuming compliance procedures. We have not yet received marketing
approval for any of our internally developed proprietary products. Our
proprietary drugs and products will require lengthy clinical trials along with
FDA and comparable foreign agency review as new drugs. Our generic drugs will
also require regulatory review and approval.

    We cannot predict with certainty if or when we might submit for regulatory
review those products currently under development. Once we submit our potential
products for review, we cannot assure you that the FDA or other regulatory
agencies will grant approvals for any of our pharmaceutical products on a timely
basis or at all. Sales of our products outside the United States will be subject
to regulatory requirements governing clinical trials and marketing approval.
These requirements vary widely from country to country and could delay the
introduction of our products in those countries.

    IF OUR RELATIONSHIP WITH ABBOTT IS NOT SUCCESSFUL, OUR BUSINESS COULD BE
HARMED. Our strategic relationship with Abbott is important to our success.
However, that relationship may not be successful. We cannot assure you that we
will receive any additional payments from Abbott or that the relationship will
be commercially successful. The transactions contemplated by our agreements with
Abbott, including the equity purchases and cash payments, are subject to
numerous risks and conditions. For example:

    - we may fail to achieve clinical and sales milestones;

    - rubitecan may fail to achieve regulatory approval domestically and
      internationally;

    - rubitecan may not be commercially successful;

    - Abbott may fail to perform its obligations under our agreements, such as
      failing to devote sufficient resources to marketing rubitecan; and

    - our agreements with Abbott may be terminated in their entirety or on a
      territory-by-territory basis against our will.

    The occurrence of any of these events could severely harm our business.

    WE HAVE GRANTED CERTAIN RIGHTS TO ABBOTT THAT COULD NEGATIVELY AFFECT YOUR
INVESTMENT. We have granted Abbott an option to purchase shares of our common
stock so that upon its exercise Abbott will own up

                                       13
<PAGE>
to 49% of our outstanding common stock. Our ability to satisfy this contractual
obligation is subject to a number of conditions outside of our control,
including:

    - stockholder approval of an increase in the number of shares of our
      authorized common stock;

    - stockholder approval of a potential change in control under the rules of
      the Nasdaq National Market; and

    - clearance of the purchase by federal antitrust regulators.

    If we do not satisfy any of these conditions, Abbott could terminate our
relationship. If we obtain all necessary approvals and Abbott exercises its
option, the stock ownership of our other stockholders will be diluted and Abbott
will have significant influence over us. Abbott's right to exercise this option,
and Abbott's share ownership after exercise, may discourage other parties from
acquiring us.

    Abbott has a right of first discussion with respect to our product portfolio
and a right of first refusal to acquire us. These rights may discourage third
parties from bidding on any assets that we wish to sell or license and may
discourage acquisition bids. These provisions may limit the price that investors
might be willing to pay in the future for shares of our common stock.

    WE HAVE A HISTORY OF OPERATING LOSSES AND AN ACCUMULATED DEFICIT, WE MAY NOT
ACHIEVE OR MAINTAIN PROFITABILITY IN THE FUTURE, AND WE MAY NEED TO OBTAIN
ADDITIONAL FUNDING. We incurred cumulative losses of $100.4 million for the
period from inception through March 31, 2000. These losses included non-cash
charges of $18.4 million for the acquisition of in-process research and
development. Currently we are not profitable and we expect to continue to incur
substantial operating losses at least through 2000 and into 2001. Our ability to
achieve profitability will depend primarily on our ability to obtain regulatory
approval for and successfully commercialize rubitecan. Our success will also
depend, to a lesser extent, on our ability to develop and obtain regulatory
approval of Nipent for indications other than hairy cell leukemia and to bring
our proprietary products to market. Our ability to become profitable will also
depend upon a variety of other factors, including the following:

    - increases in the level of our research and development, including the
      timing and costs of any expansion of clinical trials;

    - regulatory approvals of competing products, or expanded labeling approvals
      of existing products;

    - increases in sales and marketing expenses related to the commercial launch
      of rubitecan;

    - delays in or inadequate commercial sales of rubitecan, once regulatory
      approvals have been received; and

    - expenditures associated with acquiring products, technologies or companies
      and further developing these assets.

    We cannot predict the outcome of these factors and we cannot assure you that
we will ever become profitable.

    Even if we do become profitable, we may need substantial additional funding.
We expect that our rate of spending will accelerate as a result of increased
clinical trial costs and expenses associated with regulatory approval and
commercialization of our products now in development. We anticipate that our
capital resources will be adequate to fund operations and capital expenditures
at least through 2002. However, if we experience unanticipated cash requirements
during this period, we could require additional funds much sooner. Our business,
results of operations and cash flows will be adversely affected if we fail to
obtain adequate funding in a timely manner, or at all. We may receive funds from
the sale of equity securities, or the exercise of outstanding warrants and stock
options. Additionally, we may receive funds upon the achievement of certain
developmental and sales milestones pursuant to our agreement with Abbott.
However, we cannot assure you that any of those fundings will occur, or if they

                                       14
<PAGE>
occur, that they will be on terms favorable to us. Also, the dilutive effect of
those fundings could adversely affect our results per share.

    ASSERTING, DEFENDING AND MAINTAINING INTELLECTUAL PROPERTY RIGHTS COULD BE
DIFFICULT AND COSTLY AND FAILURE TO DO SO WILL HARM OUR ABILITY TO COMPETE AND
THE RESULTS OF OUR OPERATIONS. If competitors develop substantially equivalent
proprietary information and techniques or otherwise gain access to our trade
secrets, if our trade secrets are disclosed or if we cannot effectively protect
our rights to unpatented trade secrets, our business will be harmed.

    The pharmaceutical fields are characterized by a large number of patent
filings. A substantial number of patents have already been issued to other
pharmaceutical companies, research or academic institutions or others.
Competitors may have filed applications for or have been issued patents and may
obtain additional patents and proprietary rights related to products or
processes that compete with or are similar to ours. We may not be aware of all
of the patents potentially adverse to our interests that may have been issued to
others.

    We actively seek patent protection for our proprietary products and
technologies. We have a number of United States patents and also have licenses
to, or assignments of, numerous patents issued both in the United States and
elsewhere. We may also license our patents outside the United States.
Limitations on patent protection outside the United States, and differences in
what constitutes patentable subject matter in countries outside the United
States, may limit the protection we have on patents or licenses of patents
outside the United States.

    Litigation may be necessary to protect our patent position, and we cannot be
certain that we will have the required resources to pursue the necessary
litigation or otherwise to protect our patent rights. Our efforts to protect our
patents may fail. In addition to pursuing patent protection in appropriate
cases, we also rely on trade secret protection for unpatented proprietary
technology. However, trade secrets are difficult to protect. Our trade secrets
or those of our collaborators may become known or may be independently
discovered by others.

    Our proprietary products are dependent upon compliance with numerous
licenses and agreements. These licenses and agreements require us to make
royalty and other payments, reasonably exploit the underlying technology of the
applicable patents, and comply with regulatory filings. If we fail to comply
with these licenses and agreements, we could lose the underlying rights to one
or more of these potential products, which would adversely affect our business,
results of operations and cash flows.

    From time to time we receive correspondence inviting us to license patents
from third parties. Although we know of no pending patent infringement suits,
discussions regarding possible patent infringements or threats of patent
infringement litigation either related to patents held by us or our licensors or
our products or proposed products, there has been, and we believe that there
will continue to be, significant litigation in the pharmaceutical industry
regarding patent and other intellectual property rights. Claims may be brought
against us in the future based on patents held by others. These persons could
bring legal actions against us claiming damages and seeking to enjoin clinical
testing, manufacturing and marketing of the affected product. If we become
involved in any litigation, it could consume a substantial portion of our
resources, regardless of the outcome of the litigation. If any of these actions
are successful, in addition to any potential liability for damages, we could be
required to obtain a license to continue to manufacture or market the affected
product. We cannot assure you whether we would prevail in any of these actions
or that we could obtain any licenses required under any of these patents on
acceptable terms, if at all.

    IF WE LOSE KEY PERSONNEL OR ARE UNABLE TO ATTRACT AND RETAIN ADDITIONAL,
HIGHLY SKILLED PERSONNEL REQUIRED FOR THE EXPANSION OF OUR ACTIVITIES, OUR
BUSINESS WILL SUFFER. Our success is dependent on key personnel, including
Dr. Rubinfeld, our President and Chief Executive Officer, and members of our
senior management and scientific staff. To successfully expand our operations,
we will need to attract and retain

                                       15
<PAGE>
additional, highly skilled individuals, particularly in the areas of sales,
marketing, clinical administration, manufacturing and finance. We compete with
other companies for the services of existing and potential employees. We believe
our compensation and benefits packages are competitive for our geographical
region and our industry group. However, we may be at a disadvantage to the
extent that potential employees may favor larger, more established employers.

ITEM 3--QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

    Due to the short-term nature of our interest bearing assets, we believe that
our exposure to interest rate market risk is not significant.

                                       16
<PAGE>
                                 SUPERGEN, INC.
                           PART II--OTHER INFORMATION

ITEM 2. CHANGES IN SECURITIES AND USE OF PROCEEDS

RECENT SALES OF UNREGISTERED SECURITIES

    In January 2000, we issued 933,394 shares of unregistered common stock to
Abbott Laboratories in connection with the Worldwide Sales, Distribution, and
Development Agreement, dated as of December 21, 1999 and covering rubitecan. We
received $26,500,000 from Abbott in exchange for the shares of our common stock.

    The issuance of shares described above was in reliance on Section 4(2) of
the Securities Act of 1933, as amended.

    We made no public solicitation in connection with the issuance of the above
mentioned securities. We relied on representations from Abbott that they
purchased the securities for investment for their own account and not with a
view to, or for resale in connection with, any distribution thereof and that
they were aware of our business affairs and financial condition and had
sufficient information to reach an informed and knowledgeable decision regarding
their acquisition of the securities.

USE OF PROCEEDS

    On March 13, 1996, we commenced our initial public offering (the "IPO") of
4,025,000 units, which included the underwriter's over-allotment option of
525,000 units at a public offering price of $6.00 per unit. A unit consisted of
one share of our common stock $0.001 par value per share, and a warrant to
purchase one share of our common stock at $9.00. We commenced the IPO pursuant
to a registration statement on Form S-B (file no. 333-476 LA) filed with the
Securities and Exchange Commission. Of the units registered, 4,024,302 were
sold. Paulson Investment Company was the managing underwriter of the IPO.
Aggregate gross proceeds from the IPO (prior to deduction of underwriting
discounts and commissions and expenses of the offering and any exercises of the
warrants) were $24,146,000. All of the shares registered for the exercise of the
warrants have not yet been sold. There were no selling stockholders in the IPO.

    We paid total expenses of $2,615,000 in connection with the IPO, consisting
of underwriting discounts, commissions and expenses of $1,992,000 and other
expenses of approximately $623,000. The net proceeds from the IPO through
March 31, 2000, including subsequent exercises of warrants to purchase common
stock, were $44,468,000.

    From March 13, 1996, the effective date of the registration statement, to
March 31, 2000, (our fiscal 2000 first quarter end), the approximate amount of
net proceeds used were:

<TABLE>
<CAPTION>

<S>                                                           <C>
Construction of plant, building and facilities..............  $ 1,246,000
Purchase and installation of machinery and equipment........      295,000
Purchase of real estate.....................................      744,000
Working capital used in operations..........................   37,906,000
Repurchase of common stock..................................    3,557,000
Purchase of equity investment...............................      500,000
Acquisition of developed technology.........................      220,000
</TABLE>

                                       17
<PAGE>
    None of such payments consisted of direct or indirect payments to directors,
officers, owners of more than 10% of the outstanding stock of the Company or
affiliates of the Company, with the exception of:

    - The payment to repurchase common stock, which was made to a stockholder
      that, immediately prior to the repurchase, owned more than 10% of our then
      outstanding common stock; and

    - Payments to directors and officers as compensation for services provided.

    On September 20, 1999, we issued a notice that we would redeem our 1996
publicly traded $9.00 warrants ("SUPGW" warrants) outstanding at April 16, 2000
at $0.25 per warrant. During the quarter ended March 31, 2000, 1,623,000 of the
SUPGW warrants were exercised, resulting in proceeds to the Company of
approximately $14,600,000. Also during the quarter, we received an additional
$4,500,000 upon exercise of underwriters' warrants that had been issued in
connection with our IPO.

ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K

<TABLE>
<S>  <C>
(a)  Exhibit No.

     27.1  Financial Data Schedule--electronic filing only.

     The following reports were filed on Form 8-K during the
(b)  quarter for which this report is filed.

         - Form 8-K/A dated December 22, 1999, filed on
         January 7, 2000 regarding our agreements with Abbott
           Laboratories dated December 21, 1999.

         - Form 8-K/A dated December 22, 1999, filed on
         March 16, 2000 regarding our agreements with Abbott
           Laboratories dated December 21, 1999.
</TABLE>

                                       18
<PAGE>
                                   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.

<TABLE>
<S>                                                    <C>  <C>
                                                       SUPERGEN, INC.

                                                       By:             /s/ RONALD H. SPAIR
                                                            -----------------------------------------
                                                                         Ronald H. Spair
                                                            SENIOR VICE PRESIDENT AND CHIEF FINANCIAL
                                                                 OFFICER (PRINCIPAL FINANCIAL AND
Date: May 16, 2000                                                     ACCOUNTING OFFICER)
</TABLE>

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