<PAGE>
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                                 UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

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

                                   FORM 10-Q

<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 SEPTEMBER 30, 1999

                                       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
   of incorporation or organization)                  Identification Number)

     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
November 3, 1999, was 24,952,937.

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<PAGE>
                               TABLE OF CONTENTS

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

       Item 1-- Financial Statements (Unaudited)

               Consolidated Balance Sheets as of
               September 30, 1999 and December 31, 1998.....  3

               Consolidated Statements of Operations for the
               three and nine month periods
                 ended September 30, 1999 and 1998..........  4

               Consolidated Statements of Cash Flows for the
               nine month periods ended
                 September 30, 1999 and 1998................  5

               Notes to Consolidated Financial Statements...  6

       Item 2-- Management's Discussion and Analysis of
       Financial Condition and
                 Results of Operations......................  12

       Item 3--Quantitative and Qualitative Disclosures of
       Market Risk..........................................  20

PART II        OTHER INFORMATION

       Item 2--Changes in Securities and Use of Proceeds....  21

       Item 6--Exhibits and Reports on Form 8-K.............  23

SIGNATURES..................................................  24
</TABLE>

                                       2
<PAGE>
                                 SUPERGEN, INC.

                          CONSOLIDATED BALANCE SHEETS

               (IN THOUSANDS, EXCEPT SHARE AND PER SHARE AMOUNTS)

<TABLE>
<CAPTION>
                                                              SEPTEMBER 30,   DECEMBER 31,
                                                                  1999            1998
                                                              -------------   ------------
                                                               (UNAUDITED)      (NOTE 1)
<S>                                                           <C>             <C>
                           ASSETS
Current assets:
  Cash and cash equivalents.................................    $ 31,844        $  8,614
  Marketable securities.....................................       1,042           3,299
  Accounts receivable, net..................................         970             712
  Inventories...............................................       1,631           1,245
  Due from related parties..................................         121              91
  Prepaid expenses and other current assets.................       2,257             615
                                                                --------        --------
    Total current assets....................................      37,865          14,576

Property, plant and equipment, net..........................       2,816           2,939
Developed technology at cost, net...........................       1,811           1,266
Goodwill and other intangibles, net.........................       2,175              --
Investment in preferred stock of related party..............         500             500
Due from related party......................................         450             450
Other assets................................................       1,145              62
                                                                --------        --------
    Total assets............................................    $ 46,762        $ 19,793
                                                                ========        ========
            LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
  Accounts payable and accrued liabilities..................    $  2,527        $  2,451
  Accrued employee benefits.................................         704             524
                                                                --------        --------
    Total current liabilities...............................       3,231           2,975

Stockholders' equity:
  Preferred stock, $.001 par value; 2,000,000 shares
    authorized; none outstanding............................          --              --
  Common stock, $.001 par value; 40,000,000 shares
    authorized; 24,749,736 and 20,969,953 shares issued and
    outstanding at September 30, 1999 and December 31, 1998,
    respectively............................................          25              21
  Additional paid in capital................................     128,777          72,818
  Deferred compensation.....................................        (892)             --
  Accumulated other comprehensive loss......................        (106)           (128)
  Accumulated deficit.......................................     (84,273)        (55,893)
                                                                --------        --------
    Total stockholders' equity..............................      43,531          16,818
                                                                --------        --------
    Total liabilities and stockholders' equity..............    $ 46,762        $ 19,793
                                                                ========        ========
</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     NINE MONTHS ENDED
                                                           SEPTEMBER 30,         SEPTEMBER 30,
                                                        -------------------   -------------------
                                                          1999       1998       1999       1998
                                                        --------   --------   --------   --------
<S>                                                     <C>        <C>        <C>        <C>
Net sales.............................................  $    736   $   537    $  3,076   $  2,089
Operating expenses:
  Cost of sales.......................................       131       739       1,324      1,327
  Research and development............................     3,934     2,592      10,730      7,630
  Sales and marketing.................................     1,774       738       4,239      2,185
  General and administrative..........................     1,198       947       2,838      2,885
  Acquisition of in-process research and
    development.......................................    10,850        --      10,850         --
                                                        --------   -------    --------   --------
    Total operating expenses..........................    17,887     5,016      29,981     14,027
                                                        --------   -------    --------   --------

Loss from operations..................................   (17,151)   (4,479)    (26,905)   (11,938)
Interest income.......................................       241       205         525        742
Amortization of prepaid loan commitment fee...........    (1,304)       --      (2,000)        --
                                                        --------   -------    --------   --------
Net loss..............................................  $(18,214)  $(4,274)   $(28,380)  $(11,196)
                                                        ========   =======    ========   ========
Basic net loss per share..............................  $  (0.78)  $ (0.21)   $  (1.29)  $  (0.55)
                                                        ========   =======    ========   ========
Weighted average shares used in basic net loss per
  share calculation...................................    23,307    20,379      21,993     20,326
                                                        ========   =======    ========   ========
</TABLE>

          See accompanying notes to consolidated financial statements

                                       4
<PAGE>
                                 SUPERGEN, INC.

                     CONSOLIDATED STATEMENTS OF CASH FLOWS

                                 (IN THOUSANDS)

                                  (UNAUDITED)

<TABLE>
<CAPTION>
                                                               NINE MONTHS ENDED
                                                                 SEPTEMBER 30,
                                                              -------------------
                                                                1999       1998
                                                              --------   --------
<S>                                                           <C>        <C>
Operating activities:
  Net loss..................................................  $(28,380)  $(11,196)
  Adjustments to reconcile net loss to net cash used in
    operating activities:
    Depreciation and amortization...........................       578        417
    Amortization of prepaid loan commitment fee.............     2,000         --
    Expense related to stock options and warrants granted to
      non-employees.........................................     1,244        170
    Non-cash charges related to acquisition of in-process
      research and development..............................    10,850         --
    Changes in operating assets and liabilities:
      Accounts receivable...................................      (221)      (304)
      Inventories...........................................      (386)       462
      Prepaid expenses and other assets.....................    (1,625)      (927)
      Accounts payable and other liabilities................       (12)     1,051
      Due from related parties..............................       (30)       105
                                                              --------   --------
Net cash used in operating activities.......................   (15,982)   (10,222)

Investing activities:
  Purchase of marketable securities.........................    (1,033)    (5,353)
  Sale of marketable securities.............................     2,240      1,076
  Purchase of property and equipment........................      (206)      (637)
  Acquisition of cash due to purchase of Sparta
    Pharmaceuticals.........................................       510         --
                                                              --------   --------
Net cash provided by (used in) investing activities.........     1,511     (4,914)

Financing activities:
  Issuance of common stock, net of issuance costs...........    37,701        190
                                                              --------   --------
Cash provided by financing activities.......................    37,701        190
                                                              --------   --------
Net increase (decrease) in cash and cash equivalents........    23,230    (14,946)
Cash and cash equivalents at beginning of period............     8,614     23,326
                                                              --------   --------
Cash and cash equivalents at end of period..................  $ 31,844   $  8,380
                                                              ========   ========
</TABLE>

          See accompanying notes to consolidated financial statements

                                       5
<PAGE>
                                 SUPERGEN, INC.

                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS

                               SEPTEMBER 30, 1999

                                  (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, 1998 and in accordance with the instructions to
Form 10-Q. The consolidated financial statements include the accounts of Sparta
Pharmaceuticals, Inc. ("Sparta") from August 12, 1999, the date of acquisition,
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, 1998 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, 1998.

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
September 30, 1999 (in thousands):

<TABLE>
<CAPTION>
                                                                            GROSS
                                                              AMORTIZED   UNREALIZED   ESTIMATED
                                                                COST        LOSSES     FAIR VALUE
                                                              ---------   ----------   ----------
<S>                                                           <C>         <C>          <C>
U.S. corporate debt securities..............................   $24,254       $  (5)     $24,249
Marketable equity security..................................       167        (101)          66
                                                               -------       -----      -------
      Total.................................................   $24,421       $(106)     $24,315
                                                               =======       =====      =======
</TABLE>

<TABLE>
<CAPTION>
                                                                            GROSS
                                                              AMORTIZED   UNREALIZED   ESTIMATED
                                                                COST        LOSSES     FAIR VALUE
                                                              ---------   ----------   ----------
<S>                                                           <C>         <C>          <C>
Amounts included in cash and cash equivalents...............   $22,177       $  (3)     $22,174
Marketable securities, current..............................     1,043          (1)       1,042
Amounts included in other assets............................     1,201        (102)       1,099
                                                               -------       -----      -------
      Total.................................................   $24,421       $(106)     $24,315
                                                               =======       =====      =======
</TABLE>

                                       6
<PAGE>
                                 SUPERGEN, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

                               SEPTEMBER 30, 1999

                                  (UNAUDITED)

NOTE 2.  CASH, CASH EQUIVALENTS, AND MARKETABLE SECURITIES (CONTINUED)

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

<TABLE>
<CAPTION>
                                                      SEPTEMBER 30,   DECEMBER 31,
                                                          1999            1998
                                                      -------------   ------------
<S>                                                   <C>             <C>
Debt securities:
Due in one year or less.............................     $23,216         $1,391
Due after one year through three years..............       1,033          2,065
                                                         -------         ------
                                                          24,249          3,456
Marketable equity security..........................          66             26
                                                         -------         ------
      Total.........................................     $24,315         $3,482
                                                         =======         ======
</TABLE>

    Realized gains and losses for the nine months ended September 30, 1999 and
1998 were not material.

NOTE 3.  INVENTORIES

    Inventories consist of the following (in thousands):

<TABLE>
<CAPTION>
                                                      SEPTEMBER 30,   DECEMBER 31,
                                                          1999            1998
                                                      -------------   ------------
<S>                                                   <C>             <C>
Raw material........................................     $  204          $  210
Work in process.....................................        996             511
Finished goods......................................        431             524
                                                         ------          ------
                                                         $1,631          $1,245
                                                         ======          ======
</TABLE>

NOTE 4.  ACQUISITION ACTIVITY AND RELATED IN-PROCESS RESEARCH AND
  DEVELOPMENT

SPARTA PHARMACEUTICALS, INC.

    In August 1999, we completed our acquisition of Sparta
Pharmaceuticals, Inc., a biopharmaceutical company engaged in developing
technologies and drugs for the treatment of a number of life-threatening
diseases, including cancer, cardiovascular disorders, chronic metabolic
diseases, and inflammation.

    On the effective date of the merger Sparta became a wholly-owned subsidiary
of the Company. The Company issued 429,055 shares of its common stock, with a
fair value of $7,800,000, and 220,945 common stock warrants, with a fair value
of $1,558,000, to former Sparta stockholders. The Company assumed approximately
2.9 million options and warrants to purchase Sparta common stock and converted
such options to SuperGen options and warrants to acquire approximately 110,600
shares of SuperGen common stock. The $12,000 value of the options assumed is
included in the purchase price and as a component of stockholders' equity in the
consolidated financial statements. Additionally, the Company recorded
transaction related costs of approximately $262,000, which when aggregated with
the above consideration brings the total cost of the acquisition to $9,632,000.

                                       7
<PAGE>
                                 SUPERGEN, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

                               SEPTEMBER 30, 1999

                                  (UNAUDITED)

NOTE 4.  ACQUISITION ACTIVITY AND RELATED IN-PROCESS RESEARCH AND
  DEVELOPMENT (CONTINUED)

    The acquisition has been accounted for by the purchase method of accounting
and, accordingly, the results of operations of Sparta for the period from
August 12, 1999 are included in the accompanying consolidated financial
statements. Assets acquired and liabilities assumed have been recorded at their
estimated fair values. Approximately $7,450,000 of the purchase price was
allocated to acquired in-process research and development ("IPR&D"). The Sparta
research and development programs currently in process were valued as follows:

<TABLE>
<S>                                                           <C>
Oral anticancer drug for the treatment of breast, colorectal
  and other cancers (5-FP, a prodrug of 5-FU)...............  $3,430,000
Chronic metabolic disease drug (PZG)........................   1,380,000
SPARTAJECT-TM- method for the delivery of certain
  anti-cancer compounds.....................................   2,640,000
                                                              ----------
                                                              $7,450,000
                                                              ==========
</TABLE>

    - 5-FP--We estimate that the remaining research and development efforts will
      total more than $6 million over the next several years and that activities
      necessary to obtain regulatory approval could be completed and revenues
      begin to accrue to the Company with the projected introduction of a
      product in 2003.

    - PZG--We estimate that the remaining research and development efforts could
      total more than $30 million over the next several years and that
      activities necessary to obtain regulatory approval could be completed and
      revenues begin to accrue to the Company with the projected introduction of
      a product in 2005.

    - Spartaject-TM- Drug Delivery Technology--We estimate that remaining
      research and development efforts related to the application of the
      Spartaject-TM- Drug Delivery Technology to busulfan for use in bone marrow
      ablation and for the treatment of neoplastic meningitis could total more
      than $8 million over the next several years and that activities necessary
      to obtain regulatory approval could be completed and revenues begin to
      accrue to the Company with the projected introduction of a product in
      2001.

    Acquired in-process research and development represents the value assigned
in a purchase business combination to research and development projects of the
acquired business that were commenced but not yet completed at the date of
acquisition and which, if unsuccessful, have no alternative future use in
research and development activities or otherwise. In accordance with Statement
of Financial Accounting Standards No. 2 "Accounting for Research and Development
Costs," as interpreted by FASB Interpretation No. 4, amounts assigned to
acquired in-process research and development meeting the above criteria must be
charged to expense at the date of consummation of the purchase business
combination. Accordingly, we recorded a non-recurring charge for this acquired
in-process research and development at the date of acquisition.

    The allocation of the purchase price for Sparta resulted in goodwill of
approximately $1.4 million and intangibles and work force value of $500,000.
Goodwill and intangibles will be amortized over five years and work force value
over six months.

                                       8
<PAGE>
                                 SUPERGEN, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

                               SEPTEMBER 30, 1999

                                  (UNAUDITED)

NOTE 4.  ACQUISITION ACTIVITY AND RELATED IN-PROCESS RESEARCH AND
  DEVELOPMENT (CONTINUED)

DECITABINE

    In September 1999, we acquired the worldwide rights to decitabine, a
chemotherapeutic agent owned by Pharmachemie B.V., a subsidiary of Teva
Pharmaceuticals. Decitabine, which has received "orphan drug" status from the
U.S. Food and Drug Administration (the "FDA"), is currently in clinical testing
for acute leukemias and other hematological malignancies. Each year, over 50,000
new cases of acute leukemias and hematological malignancies are reported in the
United States. The FDA has not granted marketing approval to use decitabine for
the treatment of any disease.

    The acquisition involved an exchange of 171,123 shares of unregistered
SuperGen common stock valued at $3,400,000, which we charged to IPR&D. In
assigning the purchase price to IPR&D, we considered, among other factors, our
intentions for the future use of the acquired project, its stage of completion,
the lack of alternative future uses of the technology, and that no other
tangible or intangible assets were acquired. We believe decitabine has a unique
mechanism of action that may demonstrate its effectiveness in acute leukemias
and other hematological malignancies. We currently estimate that the completion
of the clinical trials and submission to the FDA of a New Drug Application could
occur in 2002 and the approximate research and development costs to complete
those processes will total $6 to $8 million. Revenues could begin with the
introduction of a product in 2002.

SURFACE SAFE-TM- PRODUCT LINE ACQUISITION

    On July 1, 1999, SuperGen acquired the Surface Safe-TM- product line from
Aldorr Inc., a medical technology development company. Surface Safe-TM-is a
two-step towelette disposable cleaning system used to decontaminate work
surfaces where chemotherapeutic preparation is conducted. Aldorr assigned to
SuperGen patents and trademarks related to the Surface Safe-TM- product line and
granted to SuperGen an irrevocable, exclusive, worldwide, perpetual and
royalty-free license to use the licensed know-how and any other intellectual
property owned or licensed by Aldorr related to the Surface Safe-TM- product
line. Aldorr will provide technology transfer assistance over a brief
transitional period and has agreed not to compete with the Company in this
marketplace for a period of five years. SuperGen also obtained a customer list
from Aldorr, Inc. The aggregate value of the 79,546 shares of unregistered
SuperGen common stock paid to Aldorr, Inc. was estimated to be $1,040,000, and
was allocated to the covenant not to compete, the customer list, trademark, and
the developed technology based on estimated fair values on the acquisition date.
The recorded assets will be amortized over five years.

NOTE 5.  STOCKHOLDERS' EQUITY

    On August 9, 1999, we issued 463,600 shares of registered common stock to an
institutional investor. As part of this transaction we also issued to the
investor three-year warrants to purchase 231,800 shares of common stock at a
price of $18.00 per share and granted registration rights in connection with
these warrants. As partial compensation to the placement agent, we issued 25,498
five-year warrants to purchase unregistered common stock at $18.00 per share.
After deducting $414,000 in commissions and fees from the gross proceeds of
$7,520,000, the net proceeds from this transaction totaled $7,106,000.

                                       9
<PAGE>
                                 SUPERGEN, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

                               SEPTEMBER 30, 1999

                                  (UNAUDITED)

NOTE 5.  STOCKHOLDERS' EQUITY (CONTINUED)

    On September 1, 1999, we issued 561,000 shares of unregistered common stock
to an institutional investor. As part of this transaction we also issued to the
investor three-year warrants to purchase 336,600 shares of our common stock at a
price of $20.00 per share. As partial compensation to the placement agent, we
issued 30,855 five-year warrants to purchase unregistered common stock at $20.00
per share. After deducting $500,000 in commissions and fees from the gross
proceeds of $9,099,000, the net proceeds from this transaction totaled
$8,599,000.

    On September 17, 1999, we issued 469,819 shares of unregistered common stock
to a group of institutional investors. As part of this transaction we also
issued to the investors three-year warrants to purchase 140,946 shares of our
common stock at a price of $22.50 per share. Additionally, the investors were
issued two-year warrants to purchase an aggregate of 140,946 shares of our
common stock, with 46,981, 46,981 and 46,984 warrants having exercise prices of
$30, $45 and $60 per share, respectively. As partial compensation to the
placement agent, we issued five-year warrants to purchase 26,161 shares of our
common stock at $22.075 per share. After deducting $495,000 in commissions and
fees from the gross proceeds of $8,250,000, the net proceeds from this
transaction totaled $7,755,000.

    On September 27, 1999, we issued 64,243 shares of unregistered common stock
to an institutional investor. As part of this transaction we also issued
three-year warrants to purchase 19,273 shares of our common stock at a price of
$22.1875 per share. Additionally, the investor was issued two-year warrants to
purchase an aggregate of 19,273 shares of our common stock, with 6,244, 6,244
and 6,245 warrants having exercise prices of $30, $45 and $60 per share,
respectively. As partial compensation to the placement agent, we issued
five-year warrants to purchase 3,975 shares of our common stock at $22.01 per
share. After deducting $75,000 in commissions and fees from the gross proceeds
of $1,250,000, the net proceeds from this transaction totaled $1,175,000.

    The stock issuance transactions noted above reflected discounts to the
market price of our stock at the transaction dates. These discounts resulted
from prior discussions with the investors and the selling prices per share were
based on a negotiated average market price. We believe that the selling prices
were reasonable in light of the volatility of our stock price, the magnitude of
the transactions, and our capital needs.

NOTE 6.  COMPREHENSIVE LOSS

    For the three months ended September 30, 1999 and 1998, total comprehensive
losses amounted to $18,221,000 and $4,257,000, respectively. For the nine months
ended September 30, 1999 and 1998, total comprehensive losses amounted to
$28,358,000 and $11,218,000, respectively.

NOTE 7.  BASIC NET LOSS PER SHARE

    We compute basic net loss per share by dividing our net loss by the weighted
average number of shares outstanding during each period. The exercise of options
and warrants is not assumed since the result would be antidilutive.

                                       10
<PAGE>
                                 SUPERGEN, INC.

             NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (CONTINUED)

                               SEPTEMBER 30, 1999

                                  (UNAUDITED)

NOTE 8.  RELATED PARTY TRANSACTION

    In September 1999, the Company and Tako Ventures, LLC ("Tako"), an
investment entity controlled by a director of the Company, agreed to terminate a
promissory note entered into earlier in the year thereby releasing any security
interest that Tako had in the assets of the Company. In connection with the
original transaction, the Company issued Tako a warrant to acquire unregistered
common stock of the Company. The value of this warrant was calculated to be
$2 million and recorded as a Prepaid Loan Commitment Fee. The Company was
amortizing this non-cash charge to operations through December 1999. The
termination of the note accelerates the amortization of the remaining loan
commitment fee of $1,304,000 into the quarter ended September 30, 1999.

NOTE 9.  SUBSEQUENT EVENT

    In November 1999, the Company and the Stehlin Foundation for Cancer Research
("Stehlin") entered into an amendment to their License Agreement dated
September 3, 1997. Pursuant to this amendment, the required aggregate payments
to Stehlin for funded research will be increased to $9.6 million. Additionally,
the amendment modifies: (i) the requirements related to the payment of cash or
stock upon the achievement of specified regulatory and marketing milestones, and
(ii) royalties on product sales.

                                       11
<PAGE>
ITEM 2.

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

PRELIMINARY NOTE REGARDING FORWARD-LOOKING STATEMENTS

    THIS QUARTERLY REPORT ON FORM 10-Q CONTAINS FORWARD-LOOKING STATEMENTS
WITHIN THE MEANING OF SECTION 27A OF THE SECURITIES ACT OF 1933, AS AMENDED, AND
SECTION 21E OF THE SECURITIES EXCHANGE ACT OF 1934, AS AMENDED. THESE
FORWARD-LOOKING STATEMENTS REPRESENT OUR EXPECTATIONS OR BELIEFS CONCERNING
FUTURE EVENTS AND INCLUDE STATEMENTS, AMONG OTHERS, REGARDING:

    - THE ADEQUACY OF OUR EXISTING CAPITAL RESOURCES

    - THE TIMING AND PROGRESS OF THE DEVELOPMENT OF OUR PROPOSED PRODUCTS,

    - FILING FOR AND RECEIVING REGULATORY APPROVALS,

    - ACQUIRING ADDITIONAL PRODUCTS AND TECHNOLOGIES,

    - ANTICIPATING THE MARKET OPPORTUNITIES FOR OUR EXTRA AND PROPRIETARY
      PRODUCTS,

    - MARKETING CURRENT AND PROPOSED PRODUCTS TO HOSPITAL BUYING GROUPS AND
      OTHERS,

    - DEVELOPING PARTNERSHIP RELATIONSHIPS,

    - INCURRING OPERATING EXPENSES AND LOSSES AND REQUIRING ADDITIONAL CAPITAL.

    ACTUAL RESULTS COULD DIFFER MATERIALLY FROM THOSE PROJECTED IN THE
FORWARD-LOOKING STATEMENTS AS A RESULT OF A VARIETY OF FACTORS, INCLUDING THOSE
SET FORTH UNDER "MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND
RESULTS OF OPERATIONS-FACTORS AFFECTING FUTURE OPERATING RESULTS" AND ELSEWHERE
IN THIS REPORT.

OVERVIEW

    We are an emerging pharmaceutical company dedicated to the acquisition,
rapid development and commercialization of products for the treatment of
life-threatening diseases, particularly cancer. We seek to minimize the time,
expense, and technical risk associated with drug commercialization by
identifying, acquiring, and developing pharmaceutical compounds in the later
stages of development, rather than committing significant resources to the
research phase of drug discovery.

    We are focusing our existing and proposed commercialization efforts on
Nipent-Registered Trademark-, Mitomycin and rubitecan (formerly known as RFS
2000).

    We are currently marketing Nipent-Registered Trademark- in the United States
for the treatment of hairy cell leukemia. We are also conducting clinical trials
of Nipent-Registered Trademark- to seek FDA approval to expand its use for the
treatment of additional forms of leukemia.

    In April 1998, we received FDA approval to market the generic drug mitomycin
for injection. Mitomycin, originally developed and marketed by Bristol-Myers
Squibb under the trade name Mutamycin-Registered Trademark-, is approved in the
United States for the treatment of adenocarcinoma of the stomach and pancreas in
combination with other approved chemotherapeutics. We began to sell mitomycin in
June 1998.

    Rubitecan is a drug compound in the late stage of clinical development.
Clinical studies indicate it has the potential to treat a variety of solid
tumors such as pancreatic, breast, lung, colorectal, ovarian, and prostate
cancers and hematological disorders.

                                       12
<PAGE>
    We are also developing our product line of enhanced generic anticancer drugs
using our Extra proprietary drug delivery technology. This technology,
consisting of a delivery system incorporating the active ingredient
cyclodextrin, has the following properties:

    - The form of a ready to inject, stable solution that increases the ease and
      safety of administration.

    - Increased shelf life, facilitating multiple doses from a single vial.

    - Less susceptibility to ulceration at the injection site due to shielding
      properties of the Extra formulation. The drug is released only upon
      circulation within the bloodstream.

    Our Extra technology is protected by a combination of exclusive and
non-exclusive licenses and related patents. These patents were issued between
1991 and 1998. The licenses pertaining to the Extra platform generally are
effective for the terms of the related patents.

    We seek to expand our portfolio of anticancer drugs through the acquisition
of products and product candidates, or companies owning such products or
candidates, which complement our portfolio and provide us with market
opportunities.

    In August 1999, we completed our acquisition of Sparta
Pharmaceuticals, Inc., a biopharmaceutical company engaged in developing
technologies and drugs for the treatment of a number of life-threatening
diseases, including cancer, cardiovascular disorders, chronic metabolic
diseases, and inflammation. Product candidates included in Sparta's portfolio
include:

    - 5-FP, or 5-fluoro pyrimidinone, is a pyrimidinone-based prodrug that is
      converted to 5-FU, or 5-fluorouracil by the liver.

    - PZG, a drug candidate with potential utility in treating:
      hypertriglyceridemia (a lipid disorder) that is unrelated to diabetes;
      obesity; hypertension; the uremia of renal failure; and Syndrome X.

    - Spartaject-TM- Drug Delivery Technology, a drug delivery system that
      accommodates poorly water soluble and water insoluble compounds by
      encapsulating them with a fatty (phospholipid) layer.

    In September 1999, we acquired the worldwide rights to decitabine, a
chemotherapeutic agent owned by Pharmachemie B.V., a subsidiary of Teva
Pharmaceuticals. Decitabine, which has received "orphan drug" status from the
FDA, is currently in clinical testing for acute leukemias and other
hematological malignancies. Each year, over 50,000 new cases of acute leukemias
and hematological malignancies are reported in the United States. The FDA has
not granted marketing approval to use decitabine for the treatment of any
disease.

    In July 1999, we acquired the Surface Safe-TM- product line from
Aldorr Inc., a medical technology development company. Surface Safe-TM-is a
two-step towelette disposable cleaning system used to decontaminate work
surfaces where chemotherapeutic preparation is conducted. The first towelette
contains chemicals recommended by both the Centers for Disease Control (CDC) and
the Occupational Safety and Health Administration (OSHA) to clean work surfaces.
The second towelette is used to deactivate the chemicals used in the first
towelette, in order to prevent damage to work surfaces through its potent
oxidizing process. Aldorr assigned to SuperGen patents and trademarks related to
the Surface Safe-TM- product line and granted to SuperGen an irrevocable,
exclusive, worldwide, perpetual and royalty-free license to use the licensed
know-how and any other intellectual property owned or licensed by Aldorr related
to the Surface Safe-TM- product line. Aldorr will provide technology transfer
assistance over a brief transitional period and has agreed not to compete with
us in this marketplace for a period of five years. SuperGen also obtained a
customer list from Aldorr, Inc. The target market for this product includes
hospital pharmacies and cancer centers nationwide, and will be sold to these
establishments by our direct sales force.

                                       13
<PAGE>
    We also have non-oncology programs in the large market areas of anemias and
other blood cell disorders, obesity/diabetes and autoimmune diseases. We intend
to seek partnerships with larger drug companies for the development and
marketing of these non-oncology drug candidates.

    We incorporated in March 1991, as a California corporation and changed our
state of incorporation to Delaware on November 3, 1997. Our executive offices
are located at Two Annabel Lane, Suite 220, San Ramon, California 94583, and our
telephone number at that address is (925) 327-0200.

RESULTS OF OPERATIONS

    THREE MONTHS ENDED SEPTEMBER 30, 1999 COMPARED TO THREE MONTHS ENDED
SEPTEMBER 30, 1998.

    Net sales were $736,000 in the third quarter of 1999 compared to $537,000 in
the third quarter of 1998. The increase was due to higher sales volumes of
Nipent-Registered Trademark- and to a lesser extent, to sales of mitomycin,
which commenced in June 1998. Sales of chemotherapy drugs tend to decrease over
the summer months. Gross margins were 82% in 1999 compared to (38)% in 1998. In
1998, margins on sales of Nipent-Registered Trademark- were adversely affected
by a $253,000 charge to cost of sales for manufacturing capacity costs and lower
unit selling prices for sales outside North America. We are in the early stages
of Nipent-Registered Trademark-sales and manufacturing and current margins may
not be indicative of future margins due to possible variations in average
selling prices and manufacturing costs.

    Research and development expenses in the third quarter of 1999 were
$3,934,000 compared to $2,592,000 in the same period in 1998. The increased
expense was primarily due to increased manufacturing costs, increased clinical
trial expenditures for rubitecan and Nipent-Registered Trademark-, and the
corresponding increase in the research and development staff.

    Sales and marketing expenses were $1,774,000 in the third quarter of 1999
compared to $738,000 in the same period in 1998. This change was primarily due
to increased expenditures to support Nipent-Registered Trademark- sales,
including promotional materials, trades shows, and speakers programs, as well as
the costs associated with the expansion of our sales and professional services
staffs.

    General and administrative expenses were $1,198,000 in the third quarter of
1999, compared to $947,000 in the same period in 1998. The increase was due
primarily to increased expenditures for investor relations and legal services.

    Acquisition of in-process research and development amounted to $10,850,000
in the third quarter of 1999. Of this non-cash charge, $7,450,000 related to
drug candidates under development by Sparta at the time of its acquisition and
$3,400,000 related to the license of decitabine from Pharmachemie.

    In September 1999, the Company and Tako Ventures, LLC ("Tako"), an
investment entity controlled by a director of the Company, agreed to terminate a
promissory note entered into earlier in the year thereby releasing any security
interest that Tako had in the assets of the Company. In connection with the
original transaction, we issued Tako a warrant to acquire unregistered common
stock of the Company. The value of this warrant was calculated to be $2 million
and recorded as a Prepaid Loan Commitment Fee. The Company was amortizing this
non-cash charge to operations through December 1999. The termination of the note
accelerates the amortization of the remaining loan commitment fee of $1,304,000
into the quarter ended September 30, 1999.

    NINE MONTHS ENDED SEPTEMBER 30, 1999 COMPARED TO NINE MONTHS ENDED
     SEPTEMBER 30, 1998

    Net sales were $3,076,000 in the first nine months of 1999 compared to
$2,089,000 in the same period in 1998. The increase was due to higher sales
volumes of Nipent-Registered Trademark- and to a lesser extent, to sales of
mitomycin, which commenced in June 1998. Gross margins were 57% in 1999 compared
to 36% in 1998. The increase in gross margin was due primarily to a larger
percentage of Nipent-Registered Trademark- units sold in 1998 at a lower unit
selling price under a supply agreement for sales outside North America and a
$253,000 charge

                                       14
<PAGE>
in 1998 to cost of sales for manufacturing capacity costs. We are in the early
stages of Nipent-Registered Trademark- sales and manufacturing and current
margins may not be indicative of future margins due to possible variations in
average selling prices and manufacturing costs.

    Research and development expenses in the first nine months of 1999 were
$10,730,000 compared to $7,630,000 in the same period in 1998. The increased
expense was primarily due to increased manufacturing costs, increased clinical
trial expenditures for rubitecan and Nipent-Registered Trademark-, and the
corresponding increase in the research and development staff.

    Sales and marketing expenses were $4,239,000 in the first nine months of
1999 compared to $2,185,000 in the same period in 1998. The increase was
primarily due to increased expenditures to support Nipent-Registered Trademark-
sales, including promotional materials, trades shows, and speakers programs, as
well as the costs associated with the expansion of our sales and professional
services staffs.

    General and administrative expenses were $2,838,000 in the first nine months
of 1999, compared to $2,885,000 in the same period in 1998. The decline was due
a reduction in consulting fees, offset by increased expenditures for investor
relations and legal services.

    Acquisition of in-process research and development amounted to $10,850,000
in the first nine months of 1999. Of this non-cash charge, $7,450,000 related to
drug candidates under development by Sparta at the time of its acquisition and
$3,400,000 related to the license of decitabine from Pharmachemie.

    In September 1999, the Company and Tako agreed to terminate a promissory
note entered into earlier in the year thereby releasing any security interest
that Tako had in the assets of the Company. In connection with the original
transaction, we issued Tako a warrant to acquire unregistered common stock of
the Company. The Company calculated the value of the warrant to be $2 million
and recorded this amount as a Prepaid Loan Commitment Fee. The Company was
amortizing this non-cash charge to operations through December 1999. The
termination of the note accelerates the amortization of the remaining loan
commitment fee resulting in a total non-cash charge of $2 million for the first
nine months of 1999.

LIQUIDITY AND CAPITAL RESOURCES

    Our cash, cash equivalents and marketable securities totaled $32.9 million
at September 30, 1999 compared to $11.9 million at December 31, 1998.

    During the fiscal third quarter, we raised $24.6 million in cash through the
private placement of our common stock with institutional investors. This
increased the total cash raised in private placements to $36.5 million for the
nine months ended September 30, 1999. To date, we have relied on external
financings to provide the capital necessary to fund the operations of the
Company. We believe that the need for additional funding will increase in the
future and that the continued ability to raise additional funds from external
sources will be critical to the success of the Company.

    The net cash used in operating activities of $16.0 million in the first nine
months of 1999 primarily reflected the net loss for the period of
$28.4 million, offset by non-cash charges of approximately $14.1 million related
to the acquisition of in-process research and development, amortization of
prepaid loan commitment fees, and charges related to stock options and warrants
granted to non-employees.

    We believe that our current cash, cash equivalents, and investments in debt
securities will satisfy our cash requirements at least through December 31,
2000. Our primary planned uses of cash during that period are:

    - Funding operations;

    - Conducting clinical testing of rubitecan, Nipent-Registered Trademark- and
      other product candidates;

    - Marketing for expanded indications for Nipent-Registered Trademark- that
      may be developed; and

    - Continuing other research and development programs.

                                       15
<PAGE>
    As of September 20, 1999, the closing bid price of our common stock for the
preceding twenty consecutive trading days exceeded $18.00 per share. Under the
terms of the Warrant Agreement, dated March 12, 1996, between us and ChaseMellon
Shareholder Services LLC (the successor to First Interstate Bank of California),
on September 20, 1999 we were entitled to give notice of the redemption of
warrants issued under the Warrant Agreement (the "Warrants") that are
outstanding at a time at least thirty days from the date of our redemption
notice. Accordingly, on September 20, 1999 we gave notice to all Warrant holders
and to ChaseMellon Shareholder Services LLC that we will redeem all outstanding
Warrants on April 16, 2000. All rights of Warrant holders other than the right
to receive the redemption price per Warrant equal to $0.25 per Warrant will
terminate from and after April 16, 2000. Based on the number of Warrants
outstanding on November 3, 1999, the exercise of the outstanding Warrants could
result in an additional $34.0 million in cash for the Company and the issuance
of an additional 3,785,917 shares of common stock. See "The Redemption of Our
Outstanding Public Warrants May Cause the Price of Our Common Stock to Fall and
May Result in Dilution."

    During the third quarter, we terminated a promissory note that provided up
to $5 million in available capital to the Company. The termination of the
promissory note eliminated any security interest in the assets of the Company
available to the note holder.

    During the third quarter, we acquired a number of product candidates in
clinical trials through our acquisition of Sparta Pharmaceuticals, Inc. and our
acquisition of decitabine from Pharmachemie. These product candidates will
require significant additional expenditures to complete the clinical development
necessary to gain marketing approval from the FDA and equivalent foreign
regulatory agencies. The pace at which we develop these product candidates will
be constrained by availability of the human and financial resources necessary to
complete the regulatory process.

    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 in 2000.

    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. See "We Will Need
Additional Funding Which May Not Be Readily Available."

ACQUISITION OF IN-PROCESS RESEARCH AND DEVELOPMENT AND RELATED ASSETS

SPARTA DRUG CANDIDATES

    In August 1999, we completed our acquisition of Sparta
Pharmaceuticals, Inc., a biopharmaceutical company engaged in developing
technologies and drugs for the treatment of a number of life-threatening
diseases, including cancer, cardiovascular disorders, chronic metabolic
diseases, and inflammation.

    Approximately $7,450,000 of the purchase price was allocated to acquired
in-process research and development ("IPR&D"). The Sparta research and
development programs currently in process were valued as follows:

<TABLE>
<S>                                                           <C>
Oral anticancer drug for the treatment of breast, colorectal
  and other cancers (5-FP, a prodrug of 5-FU)...............  $3,430,000
Chronic metabolic disease drug (PZG)........................   1,380,000
SPARTAJECT method for the delivery of certain anti-cancer
  compounds.................................................   2,640,000
                                                              ----------
                                                              $7,450,000
                                                              ==========
</TABLE>

    - 5-FP, or 5-fluoro pyrimidinone, is a pyrimidinone-based prodrug that is
      converted to 5-FU, or 5-fluorouracil by the liver. Prodrug technology
      involves administering an inactive compound, known as a prodrug, which is
      absorbed in the digestive tract and is converted to an active agent in the
      liver

                                       16
<PAGE>
      by a localized enzyme. We estimate that the remaining research and
      development efforts will total more than $6 million over the next several
      years and that activities necessary to obtain regulatory approval could be
      completed and revenues begin to accrue to the Company with the projected
      introduction of a product in 2003.

    - Animal studies and early clinical studies of PZG suggest that it may help
      to control the blood sugar and lipid abnormalities of diabetes. In
      addition, the pre-clinical and clinical studies of PZG suggest that the
      drug may have utility in treating: hypertriglyceridemia (a lipid disorder)
      that is unrelated to diabetes; obesity; hypertension; the uremia of renal
      failure; and Syndrome X. We estimate that the remaining research and
      development efforts could total more than $30 million over the next
      several years and that activities necessary to obtain regulatory approval
      could be completed and revenues begin to accrue to the Company with the
      projected introduction of a product in 2005.

    - Spartaject-TM- Drug Delivery Technology is a drug delivery system that
      accommodates poorly water soluble and water insoluble compounds by
      encapsulating them with a fatty (phospholipid) layer. Currently, there are
      ongoing clinical trials applying the Spartaject-TM- Drug Delivery
      Technology to busulfan for use in bone marrow ablation and for the
      treatment of neoplastic meningitis. We estimate that remaining research
      and development efforts could total more than $8 million over the next
      several years and that activities necessary to obtain regulatory approval
      could be completed and revenues begin to accrue to the Company with the
      projected introduction of a product in 2001.

DECITABINE

    In September 1999, we acquired the worldwide rights to decitabine, a
chemotherapeutic agent owned by Pharmachemie B.V., a subsidiary of Teva
Pharmaceuticals. Decitabine, which has received "orphan drug" status from the
U.S. Food and Drug Administration (the "FDA"), is currently in clinical testing
for acute leukemias and other hematological malignancies. Each year, over 50,000
new cases of acute leukemias and hematological malignancies are reported in the
United States. The FDA has not granted marketing approval to use decitabine for
the treatment of any disease.

    The acquisition involved an exchange of 171,123 shares of unregistered
SuperGen common stock valued at $3,400,000, which we charged to IPR&D. In
assigning the purchase price to IPR&D, we considered, among other factors, our
intentions for the future use of the acquired project, its stage of completion,
the lack of alternative future uses of the technology, and that no other
tangible or intangible assets were acquired. We believe decitabine has a unique
mechanism of action that may demonstrate its effectiveness in acute leukemias
and other hematological malignancies. We currently estimate that the completion
of the clinical trials and submission to the FDA of a New Drug Application could
occur in 2002 and the approximate research and development costs to complete
those processes will total $6 to $8 million. Revenues could begin with the
introduction of a product in 2002.

FACTORS CONSIDERED WHEN EVALUATING IPR&D

    Acquired in-process research and development represents the value assigned
in a purchase business combination to research and development projects of the
acquired business that were commenced but not yet completed at the date of
acquisition and which, if unsuccessful, have no alternative future use in
research and development activities or otherwise. In accordance with Statement
of Financial Accounting Standards No. 2 "Accounting for Research and Development
Costs," as interpreted by FASB Interpretation No. 4, amounts assigned to
acquired in-process research and development meeting the above criteria must be
charged to expense at the date of consummation of the purchase business
combination. Accordingly, the Company recorded a non-recurring charge for this
acquired in-process research and development at the date of acquisition.

                                       17
<PAGE>
    The nature of the efforts required to develop any of the acquired IPR&D into
technologically feasible and commercially viable products principally relates to
the successful performance of additional clinical trials. Though we currently
expect that the acquired IPR&D will be successfully developed, commercial
viability of these proposed products may never be achieved. See "Factors
Affecting Future Operating Results" for further information on the risks and
uncertainties associated with the drug development and approval process, the
consequences of failure to complete or untimely completion, and other risks
associated with the completion of the above and other IPR&D projects.

FACTORS AFFECTING FUTURE OPERATING RESULTS

    THE RISKS AND UNCERTAINTIES DESCRIBED BELOW ARE NOT THE ONLY ONES FACING
SUPERGEN. ADDITIONAL RISKS AND UNCERTAINTIES NOT PRESENTLY KNOWN TO US OR THAT
WE CURRENTLY DEEM IMMATERIAL MAY ALSO IMPAIR OUR BUSINESS OPERATIONS.

    IF ANY OF THE FOLLOWING RISKS ACTUALLY OCCUR, OUR BUSINESS, RESULTS OF
OPERATIONS OR CASH FLOWS COULD BE ADVERSELY AFFECTED. IN THOSE CASES, THE
TRADING PRICE OF OUR COMMON STOCK COULD DECLINE.

    WE HAVE INCURRED LOSSES AND MAY NEVER ACHIEVE SIGNIFICANT REVENUES OR
PROFITABLE OPERATIONS. We have incurred cumulative losses of $84.3 million from
our inception through September 30, 1999. These losses included non-cash charges
of $18.4 million for the acquisition of in-process research and development. We
have not achieved profitability and expect to continue to incur substantial
operating losses at least through 2000. Substantially all of our revenues have
come from sales of Nipent-Registered Trademark-, and we expect this trend to
continue for some time. Nipent-Registered Trademark- revenues were $2.8 million
in the first nine months of 1999, $2.7 million in 1998, $1.5 million in 1997 and
$225,000 in 1996. All of these revenues resulted from commercial sales. We will
need to successfully market Nipent-Registered Trademark- for other indications
and bring other proprietary products to market to become profitable. Our ability
to become profitable will also depend upon a variety of other factors, including
the following:

    - The price, volume and timing of sales of products.

    - The mix between Nipent-Registered Trademark- sales in the United States
      and those under a supply agreement with Warner-Lambert Company for sales
      outside North America.

    - Variations in gross margins of our products, which may be affected by
      sales mix and competitive pricing pressures.

    - Regulatory approvals of new products or expanded labeling of existing
      products.

    - Changes in the level of our research and development, including the timing
      of any expansion of clinical trials. Clinical trials include the testing
      of drug compounds upon human subjects.

    - Acquisitions of products or technology.

    Our long-term success will also be affected by expenses, difficulties and
delays frequently encountered in developing and commercializing new
pharmaceutical products, competition, and the burdensome regulatory environment
in which we operate. We cannot be certain that we will ever achieve significant
revenues or profitable operations.

    OUR PROPOSED PROPRIETARY PRODUCTS WILL REQUIRE SIGNIFICANT ADDITIONAL
DEVELOPMENT.  Our proposed proprietary products are in the development rather
than the research stage. However, we must significantly develop all of our
proposed products before we can market them. Although we believe that the
results of our early stage clinical studies support further development of our
proposed proprietary products, the results we have obtained to date do not
necessarily indicate results of further testing, including controlled human
clinical testing. All of the potential proprietary products that we are
currently developing require extensive clinical testing before we can submit any
regulatory application for their commercial use.

                                       18
<PAGE>
    In contrast to our proposed proprietary products,
Nipent-Registered Trademark- and our generic version of mitomycin have been
approved for commercial use and we began sales of these drugs in 1996 and 1998,
respectively.

    OUR BUSINESS COULD SUFFER IF WE ARE UNABLE TO SUCCESSFULLY DEVELOP OUR
GENERIC PRODUCTS AND EXTRA PRODUCTS BASED ON GENERIC PRODUCTS BECAUSE THE
PATENTS FOR THE UNDERLYING DRUGS DO NOT EXPIRE.  We plan to develop and market
several generic and Extra drugs, some of which are currently protected by one or
more patents. If the existing United States patent protection for these drugs is
maintained or extended, it is unlikely that we will be able to market our own
generic and Extra versions of those drugs. We do not believe it is financially
prudent to proceed with substantial development efforts for generic or Extra
drugs if we do not know if or when existing patent protection will cease.

    WE WILL NEED ADDITIONAL FUNDING WHICH MAY NOT BE READILY AVAILABLE.  We
expect that we will need substantial additional funding. Our business, results
of operations and cash flows will be adversely affected if we fail to obtain
adequate funding in a timely manner.

    We believe that our current cash, cash equivalents and marketable
securities, will be adequate to fund operations and capital expenditures at
least through December 31, 2000. However, if we experience unanticipated cash
requirements during this period, we could require additional funds much sooner.
We may receive funds from the sale of equity securities or the exercise of
outstanding warrants and options to acquire common stock. However, those
fundings may not occur, or if they occur, they may not be on terms favorable to
us. Also, the dilutive effect of those fundings could adversely affect our
results per share.

    THE REDEMPTION OF OUR OUTSTANDING PUBLIC WARRANTS MAY CAUSE THE PRICE OF OUR
COMMON STOCK TO FALL AND MAY RESULT IN DILUTION.  On September 20, 1999, we
issued a notice of redemption of the common stock warrants (the "Warrants")
issued under the terms of the Warrant Agreement, dated March 12, 1996, between
us and ChaseMellon Shareholder Services LLC (the successor to First Interstate
Bank of California). The Warrants enable the holder to purchase shares of our
common stock at a price of $9.00 per share. As of November 3, 1999, there were
3,785,917 Warrants outstanding. We will redeem any of the Warrants that are
outstanding as of April 16, 2000 at a price of $0.25 per share. We expect that
holders of Warrants will choose to exercise the Warrants rather than have them
redeemed if the price of our common stock trades above $9.00 per share during
the period immediately preceding April 16, 2000. Our issuance of common stock at
a price of $9.00 per share may result in dilution to other holders of common
stock and may cause the price of our common stock to fall. In addition, if the
price of our common stock for the thirty day trading period following April 16,
2000 is less than $19.46, we may be required to issue additional shares of
common stock to investors that bought our common stock in privately negotiated
transactions in September 1999. Any such issuance would have a minor dilutive
effect on holders of our common stock.

    OUR BUSINESS WILL SUFFER IF WE FAIL TO OBTAIN REGULATORY APPROVALS IN A
TIMELY MANNER, IF AT ALL.  The United States Food and Drug Administration and
comparable agencies in foreign countries impose substantial requirements for the
introduction of new pharmaceutical products through lengthy and detailed
clinical testing procedures, sampling activities and other costly and
time-consuming compliance procedures. We have obtained marketing approval for
Nipent-Registered Trademark- and our internally developed generic version of
mitomycin and approval of sources of bulk drugs for our Extra and generic
products. However, we have not yet received marketing approval for any of our
internally developed proprietary products. Our proprietary drugs and Extra drugs
may require substantial clinical trials and FDA review as new drugs. Our generic
drugs require both approval of the bulk source of the drug and FDA approval of
their final formulation.

    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, the FDA or other regulatory agencies may not approve any of
our pharmaceutical products on a timely basis or at all. For example, we
initially believed that the FDA would abbreviate the approval process for our
Extra products. However, the FDA is reviewing Mito Extra, our first Extra
product submission, as a new drug. Sales of our

                                       19
<PAGE>
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.

    OUR BUSINESS WILL SUFFER IF WE ARE UNABLE TO ADEQUATELY PROTECT OUR
INTELLECTUAL PROPERTY.  Our business will be harmed 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.

    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 issued United States patents. However, 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.

    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. If we become involved in any litigation, it could
consume a substantial portion of our resources, regardless of the outcome of the
litigation.

    IF WE LOSE THE SERVICES OF CERTAIN KEY EMPLOYEES, OUR BUSINESS WILL BE
HARMED.  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 additional, highly skilled individuals, particularly in the areas of
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.

IMPACT OF THE YEAR 2000 ISSUE

    As is more fully described in our annual report on Form 10-K, we converted
to new accounting software in 1998 and that software properly recognizes dates
beyond December 31, 1999. Our assessment of the risks associated with Year 2000
are unchanged from that described in the 1998 annual report. We are in the final
stages of completing our contingency plan to address a worst case Year 2000
scenario which we intend to complete before December 31, 1999. We have received
assurances from our major business partners that their systems involving
invoicing and shipping, inventory production, and clinical trial documentation
are Year 2000 compliant.

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.

                                       20
<PAGE>
                                 SUPERGEN, INC.
                           PART II--OTHER INFORMATION

ITEM 2. CHANGES IN SECURITIES AND USE OF PROCEEDS

RECENT SALES OF UNREGISTERED SECURITIES

    On August 9, 1999, we issued 463,600 shares of registered common stock to
the SMALLCAP World Fund, Inc. ("SMALLCAP"), an institutional investor. As part
of this transaction, we also issued to the investor three-year warrants to
purchase 231,800 shares of our common stock at a price of $18.00 per share and
granted registration rights in connection with these warrants. As partial
compensation to the placement agent, we issued 25,498 five-year warrants to
purchase unregistered common stock at $18.00 per share. After deducting $414,000
in commissions and fees from the gross proceeds of $7,520,000, the net proceeds
from this transaction totaled $7,106,000.

    On September 1, 1999, we issued 561,000 shares of unregistered common stock
to SMALLCAP. As part of this transaction, we also issued to the investor
three-year warrants to purchase 336,600 shares of our common stock at a price of
$20.00 per share. As partial compensation to the placement agent, we issued to
the placement agent 30,855 five-year warrants to purchase unregistered common
stock at $20.00 per share. After deducting $500,000 in commissions and fees from
the gross proceeds of $9,099,000, the net proceeds from this transaction totaled
$8,599,000.

    On September 17, 1999, we issued 469,819 shares of unregistered common stock
to a group of institutional investors led by The Tail Wind Fund, Limited ("Tail
Wind"). As part of this transaction, we also issued to the investors three-year
warrants to purchase 140,946 shares of our common stock at a price of $22.50 per
share. Additionally, the investors were issued two-year warrants to purchase an
aggregate of 140,946 shares of our common stock, with 46,981, 46,981 and 46,984
warrants having exercise prices of $30, $45 and $60 per share, respectively. As
partial compensation to the placement agent, we issued to the placement agent
five-year warrants to purchase 26,161 shares of our common stock at $22.075 per
share. After deducting $495,000 in commissions and fees from the gross proceeds
of $8,250,000, the net proceeds from this transaction totaled $7,755,000.

    On September 27, 1999, we issued 64,243 shares of unregistered common stock
to Tail Wind. As part of this transaction, we also issued three-year warrants to
purchase 19,273 shares of our common stock at a price of $22.1875 per share.
Additionally, the investor was issued two-year warrants to purchase an aggregate
of 19,273 shares of our common stock, with 6,244, 6,244 and 6,245 warrants
having exercise prices of $30, $45 and $60 per share, respectively. As partial
compensation to the placement agent, we issued to the placement agent five-year
warrants to purchase 3,975 shares of our common stock at $22.01 per share. After
deducting $75,000 in commissions and fees from the gross proceeds of $1,250,000,
the net proceeds from this transaction totaled $1,175,000.

    The Company and the institutional investors named above entered into
purchase agreements for the aforementioned securities in reliance upon the
exemption from securities registration afforded by the provisions of
Regulation D, as promulgated by the U.S. Securities and Exchange Commission
under the Securities Act of 1933, as amended. Under all of the purchase
agreements, the Company was obligated to register the common stock sold (except
in the case of the August 9, 1999 sale to SMALLCAP) and the common stock
issuable upon exercise of most the warrants issued in connection with these
financings. The Company fulfilled its registration obligations through the
filing of a Registration Statement on Form S-3 on September 29, 1999.

    In July 1999, we issued 79,546 shares of unregistered SuperGen common stock
valued at $1,040,000 to Aldorr, Inc. in exchange for the Surface Safe-TM-
product line.

                                       21
<PAGE>
    In September 1999, we issued 171,123 shares of unregistered SuperGen common
stock valued at $3,400,000, to Pharmachemie B.V., a subsidiary of Teva
Pharmaceuticals, in exchange for the worldwide rights to decitabine, a
chemotherapeutic agent.

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 Common Stock $0.001 par value per share, and a warrant to purchase
one share of 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
September 30, 1999, including subsequent exercises of warrants to purchase
common stock, were $23,694,000.

    From March 13, 1996, the effective date of the registration statement, to
September 30, 1999, (the Company's fiscal 1999 third quarter end), the
approximate amount of net proceeds used were:

<TABLE>
<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..........................   17,132,000
Repurchase of common stock..................................    3,557,000
Purchase of equity investment...............................      500,000
Acquisition of developed technology.........................      220,000
</TABLE>

    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.

    As of September 20, 1999, the closing bid price of SuperGen, Inc. common
stock for the preceding twenty consecutive trading days exceeded $18.00 per
share. Under the terms of the Warrant Agreement, dated March 12, 1996, between
us and ChaseMellon Shareholder Services LLC (the successor to First Interstate
Bank of California), on September 20, 1999 we were entitled to give notice of
the redemption of warrants issued under the Warrant Agreement (the "Warrants")
that are outstanding at a time at least thirty days from the date of our
redemption notice. Accordingly, on September 20, 1999 we gave notice to all
Warrant holders and to ChaseMellon Shareholder Services LLC that we will redeem
all outstanding Warrants on April 16, 2000. All rights of Warrant holders other
than the right to receive the redemption price per Warrant equal to $0.25 per
Warrant will terminate from and after April 16, 2000. Our providing notice of
the redemption of the Warrants does not preclude the earlier exercise of a
Warrant by a Warrant holder as permitted under the terms of the Warrant
Agreement. The Warrants are listed for trading on the Nasdaq National Market
under the symbol "SUPGW."

                                       22
<PAGE>
ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K

    (a) Exhibit No.

<TABLE>
        <C>                     <S>                                                           <C>
               10.1*            Know-How Transfer and Cooperation Agreement dated
                                  September 10, 1999 Between the Registrant and Pharmachemie
                                  B.V.

               10.2             Agreement To Terminate and Release of Collateral dated
                                  September 30, 1999 between the Registrant and Tako
                                  Ventures, LLC.

               27.1             Financial Data Schedule--electronic filing only.

                                * Confidential treatment has been requested.
</TABLE>

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

       On August 26, 1999, the Company filed a report on Form 8-K describing its
       acquisition of Sparta Pharmaceuticals, Inc. on August 12, 1999.

                                       23
<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.

Date: November 15, 1999                                By:             /s/ JOSEPH RUBINFELD
                                                            -----------------------------------------
                                                                     Joseph Rubinfeld, Ph.D.
                                                               CHIEF EXECUTIVE OFFICER, PRESIDENT,
                                                            AND DIRECTOR (PRINCIPAL EXECUTIVE OFFICER)

Date: November 15, 1999                                By:             /s/ RONALD H. SPAIR
                                                            -----------------------------------------
                                                                         Ronald H. Spair
                                                                     CHIEF FINANCIAL OFFICER
                                                                  (PRINCIPAL FINANCIAL OFFICER)
</TABLE>

                                       24