<PAGE>
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                                 UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION
 
                             WASHINGTON, D.C. 20549
 
                            ------------------------
 
                                   FORM 10-Q
 
(MARK ONE)
 
  /X/    QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
         SECURITIES EXCHANGE ACT OF 1934
 
                 FOR THE QUARTERLY PERIOD ENDED MARCH 31, 1999
                                       OR
 
  / /    TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
         SECURITIES EXCHANGE ACT OF 1934
 
        FOR THE TRANSITION PERIOD FROM ______________ TO ______________
 
                         COMMISSION FILE NUMBER 0-27628
 
                            ------------------------
 
                                 SUPERGEN, INC.
 
             (Exact name of registrant as specified in its charter)
 
                  DELAWARE                             91-1841574
        (State or other jurisdiction                  (IRS Employer
     of incorporation or organization)             Identification No.)
 
  TWO ANNABEL LANE, SUITE 220, SAN RAMON,                 94583
                 CALIFORNIA                            (Zip Code)
  (Address of principal executive offices)
 
                                 (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 April 23, 1999, was 21,094,608.
 
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<PAGE>
                               TABLE OF CONTENTS
 
<TABLE>
<CAPTION>
                                                                                                                PAGE NO.
                                                                                                                  -----
<S>             <C>                                                                                            <C>
PART I          FINANCIAL INFORMATION
 
  Item 1 --     Financial Statements (Unaudited)
 
                Consolidated Balance Sheets as of March 31, 1999 and December 31, 1998.......................           3
 
                Consolidated Statements of Operations for the three month periods ended March 31, 1999 and
                 1998........................................................................................           4
 
                Consolidated Statements of Cash Flows for the three month periods ended March 31, 1999 and
                 1998........................................................................................           5
 
                Notes to Consolidated Financial Statements...................................................           6
 
  Item 2 --     Management's Discussion and Analysis of Financial Condition and Results of Operations........           9
 
  Item 3 --     Quantitative and Qualitative Disclosure of Market Risk.......................................          13
 
PART II         OTHER INFORMATION
 
  Item 2 --     Changes in Securities and Use of Proceeds....................................................          14
 
  Item 6 --     Exhibits and Reports on Form 8-K.............................................................          15
 
SIGNATURES...................................................................................................          16
</TABLE>
 
                                       2
<PAGE>
                                 SUPERGEN, INC.
 
                          CONSOLIDATED BALANCE SHEETS
 
               (IN THOUSANDS, EXCEPT SHARE AND PER SHARE AMOUNTS)
 
<TABLE>
<CAPTION>
                                            ASSETS
<S>                                                                    <C>          <C>
                                                                        MARCH 31,    DECEMBER
                                                                          1999          31,
                                                                       -----------     1998
                                                                                    -----------
                                                                       (UNAUDITED)
                                                                                     (NOTE 1)
Current assets:
  Cash and cash equivalents..........................................   $   5,750    $   8,614
  Marketable securities..............................................       1,253        3,299
  Accounts receivable, net...........................................         876          712
  Inventories........................................................       1,149        1,245
  Due from related parties...........................................         101           91
  Prepaid loan commitment fee........................................       1,957           --
  Prepaid expenses and other current assets..........................       1,908          615
                                                                       -----------  -----------
    Total current assets.............................................      12,994       14,576
 
Property, plant and equipment, net...................................       2,847        2,939
Developed technology at cost, net....................................       1,208        1,266
Investment in preferred stock of related party.......................         500          500
Due from related party...............................................         450          450
Other assets.........................................................         131           62
                                                                       -----------  -----------
    Total assets.....................................................   $  18,130    $  19,793
                                                                       -----------  -----------
                                                                       -----------  -----------
 
                             LIABILITIES AND STOCKHOLDERS' EQUITY
Current liabilities:
  Accounts payable and accrued liabilities...........................   $   3,259    $   2,451
  Accrued employee benefits..........................................         519          524
                                                                       -----------  -----------
    Total current liabilities........................................       3,778        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;
    21,094,608 and 20,969,953 shares issued and outstanding at March
    31, 1999 and December 31, 1998, respectively.....................          21           21
  Additional paid in capital.........................................      75,180       72,818
  Accumulated other comprehensive loss...............................         (89)        (128)
  Accumulated deficit................................................     (60,760)     (55,893)
                                                                       -----------  -----------
    Total stockholders' equity.......................................      14,352       16,818
                                                                       -----------  -----------
    Total liabilities and stockholders' equity.......................   $  18,130    $  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
                                                                                                   MARCH 31,
                                                                                              --------------------
                                                                                                1999       1998
                                                                                              ---------  ---------
<S>                                                                                           <C>        <C>
Net sales...................................................................................  $     916  $     758
 
Operating expenses:
  Cost of sales.............................................................................        708        325
  Research and development..................................................................      3,120      2,777
  Sales and marketing.......................................................................      1,232        642
  General and administrative................................................................        863      1,135
                                                                                              ---------  ---------
    Total operating expenses................................................................      5,923      4,879
                                                                                              ---------  ---------
Loss from operations........................................................................     (5,007)    (4,121)
 
Interest income.............................................................................        140        292
                                                                                              ---------  ---------
Net loss....................................................................................  $  (4,867) $  (3,829)
                                                                                              ---------  ---------
                                                                                              ---------  ---------
 
Basic net loss per share....................................................................  $   (0.23) $   (0.19)
                                                                                              ---------  ---------
                                                                                              ---------  ---------
 
Weighted average shares used in basic net loss per share calculation........................     21,063     20,235
                                                                                              ---------  ---------
                                                                                              ---------  ---------
</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,
                                                                                            --------------------
                                                                                              1999       1998
                                                                                            ---------  ---------
<S>                                                                                         <C>        <C>
Operating activities:
 
  Net loss................................................................................  $  (4,867) $  (3,829)
 
  Adjustments to reconcile net loss to net cash used in operating activities:
 
    Depreciation and amortization.........................................................        185         80
 
    Expense related to stock options and warrants granted to non-employees................         43        170
 
    Changes in operating assets and liabilities:
 
      Accounts receivable.................................................................       (164)      (114)
 
      Inventories.........................................................................         96        237
 
      Prepaid expenses and other assets...................................................     (1,312)      (253)
 
      Accounts payable and other liabilities..............................................        803        866
 
      Due from related parties............................................................        (10)        11
                                                                                            ---------  ---------
 
Net cash used in operating activities.....................................................     (5,226)    (2,832)
 
Investing activities:
 
  Purchases of marketable securities......................................................         --     (2,021)
 
  Sale of marketable securities...........................................................      2,035         --
 
  Purchase of property and equipment......................................................        (35)      (376)
                                                                                            ---------  ---------
 
Net cash provided by (used in) investing activities:......................................      2,000     (2,397)
 
Financing activities:
 
  Issuance of common stock................................................................        362        140
                                                                                            ---------  ---------
 
Cash provided by financing activities.....................................................        362        140
                                                                                            ---------  ---------
 
Net decrease in cash and cash equivalents.................................................     (2,864)    (5,089)
 
Cash and cash equivalents at beginning of period..........................................      8,614     23,326
                                                                                            ---------  ---------
 
Cash and cash equivalents at end of period................................................  $   5,750  $  18,237
                                                                                            ---------  ---------
                                                                                            ---------  ---------
</TABLE>
 
          See accompanying notes to consolidated financial statements
 
                                       5
<PAGE>
                                 SUPERGEN, INC.
                   NOTES TO CONSOLIDATED FINANCIAL STATEMENTS
                                 MARCH 31, 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 two 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 March 31,
1999 (in thousands):
 
<TABLE>
<CAPTION>
                                                                   AMORTIZED   GROSS UNREALIZED    ESTIMATED
                                                                     COST       GAINS (LOSSES)    FAIR VALUE
                                                                  -----------  -----------------  -----------
<S>                                                               <C>          <C>                <C>
U.S. corporate debt securities..................................   $   1,287       $       1       $   1,288
U.S. government debt securities.................................         202              --             202
Marketable equity security......................................         167             (90)             77
                                                                  -----------            ---      -----------
  Total.........................................................   $   1,656       $     (89)      $   1,567
                                                                  -----------            ---      -----------
                                                                  -----------            ---      -----------
</TABLE>
 
<TABLE>
<CAPTION>
                                                                   AMORTIZED   GROSS UNREALIZED    ESTIMATED
                                                                     COST       GAINS (LOSSES)    FAIR VALUE
                                                                  -----------  -----------------  -----------
<S>                                                               <C>          <C>                <C>
Amounts included in cash and cash equivalents...................   $     237       $      --       $     237
Marketable securities, current..................................       1,252               1           1,253
Amount included in other assets.................................         167             (90)             77
                                                                  -----------            ---      -----------
  Total.........................................................   $   1,656       $     (89)      $   1,567
                                                                  -----------            ---      -----------
                                                                  -----------            ---      -----------
</TABLE>
 
                                       6
<PAGE>
    Available-for-sale securities by contractual maturity are shown below (in
thousands):
 
<TABLE>
<CAPTION>
                                                                       MARCH 31,   DECEMBER 31,
                                                                         1999          1998
                                                                      -----------  -------------
<S>                                                                   <C>          <C>
Debt securities:
  Due in one year or less...........................................   $     440     $   1,391
  Due after one year through three years............................       1,050         2,065
                                                                      -----------       ------
                                                                           1,490         3,456
Marketable equity security..........................................          77            26
                                                                      -----------       ------
  Total.............................................................   $   1,567     $   3,482
                                                                      -----------       ------
                                                                      -----------       ------
</TABLE>
 
    Realized gains and losses for the three months ended March 31, 1999 and 1998
were not material.
 
NOTE 3.    INVENTORIES
 
    Inventories consist of the following (in thousands):
 
<TABLE>
<CAPTION>
                                                                       MARCH 31,   DECEMBER 31,
                                                                         1999          1998
                                                                      -----------  -------------
<S>                                                                   <C>          <C>
Raw material........................................................   $     210     $     210
Work in process.....................................................         524           511
Finished goods......................................................         415           524
                                                                      -----------       ------
                                                                       $   1,149     $   1,245
                                                                      -----------       ------
                                                                      -----------       ------
</TABLE>
 
NOTE 4.    ACQUISITION OF SPARTA PHARMACEUTICALS, INC.
 
    In January 1999, we executed an agreement to acquire Sparta Pharmaceuticals,
Inc. ("Sparta"), a biopharmaceutical company engaged in the business of
developing technologies and drugs for the treatment of a number of
life-threatening diseases, including cancer, cardiovascular disorders, chronic
metabolic diseases, and inflammation. Under the terms of the agreement, we will
acquire all of the outstanding capital stock of Sparta in exchange for 650,000
shares (subject to adjustment) of our common stock. The acquisition is subject
to the approval of Sparta stockholders and other closing conditions.
 
NOTE 5.    RELATED PARTY TRANSACTIONS
 
    Our stock purchase agreement with Tako Ventures, LLC ("Tako"), an investment
entity controlled by Lawrence J. Ellison, a director of the Company, executed in
June 1997, gave Tako certain rights to participate in future sales of common
stock at comparable terms and conditions. In December 1998, we closed a private
placement of common stock to an institutional investor at a 4% discount to a
weighted average stock price prior to the purchase. As a result, in January
1999, Tako exercised its rights and purchased 61,350 shares of unregistered
common stock for a total purchase price of $400,002. We granted Tako
registration rights in connection with this transaction.
 
    In March 1999, we executed a secured promissory note with Tako under which
we may draw up to $5 million through December 31, 1999. The interest rate for
any amounts advanced under this agreement is 10%, payable monthly, and all
principal and any unpaid interest are due on March 25, 2000. The note is secured
by substantially all our assets. At May 11, 1999, no advances had been drawn on
this note. In connection with this transaction, we issued Tako a five-year
warrant to acquire up to 500,000 shares of unregistered common stock at an
exercise price of $11.00 per share. We have calculated the value of this warrant
using the Black-Scholes valuation model. The significant inputs we used in the
model were volatility of 0.6, expected life of three years, and a risk-free
interest rate of 4.5%. The value of this warrant has been estimated at $2
million, and has been recorded in Stockholders' equity and as a Prepaid loan
 
                                       7
<PAGE>
commitment fee. This fee is being amortized through non-cash charges to
operations through December 31, 1999.
 
NOTE 6.    COMPREHENSIVE LOSS
 
    For the three months ended March 31, 1999 and 1998, total comprehensive
losses amounted to $4,828,000 and $3,864,000, 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.
 
NOTE 8.    SUBSEQUENT EVENT
 
    In April 1999, we entered into a line of credit agreement with a local bank
to borrow $3 million, secured by our $5 million certificate of deposit at that
bank. The certificate of deposit matures on September 1, 1999, and any unpaid
principal amounts advanced under the line of credit are also due on that date.
At May 11, 1999, the entire $3 million had been drawn on the line of credit.
Interest accrues at the bank's prime rate and is payable monthly.
 
                                       8
<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 two
drugs, Nipent-Registered Trademark- and 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. RFS 2000 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.
 
    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 drug 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.
 
                                       9
<PAGE>
    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 January 1999, we executed an agreement to acquire all of the
outstanding capital stock of Sparta Pharmaceuticals, Inc. for 650,000 shares
(subject to adjustment) of our common stock. The acquisition is subject to the
approval of Sparta's stockholders and is expected to close in the summer of
1999.
 
    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.
 
    THREE MONTHS ENDED MARCH 31, 1999 COMPARED TO THREE MONTHS ENDED MARCH 31,
     1998.
 
    Revenues were $916,000 in the first quarter of 1999 compared to $758,000 in
the first quarter of 1998. The increase in revenue 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 23% in 1999 compared
to 57% in 1998. The decline in gross margin was due primarily to a larger
percentage of Nipent-Registered Trademark- units sold in 1999 at a lower unit
selling price under a supply agreement for sale 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 were $3,120,000 in 1999 compared to
$2,777,000 in 1998. The increased expense was primarily due to manufacturing and
clinical costs associated with RFS 2000 and expansion of the research and
development staff.
 
    Sales and marketing expenses were $1,232,000 in 1999 compared to $642,000 in
1998. This change was primarily due to advertising and related costs to support
Nipent-Registered Trademark- sales, including approximately $375,000 for a
Nipent-Registered Trademark- symposium we held in February 1999, and the costs
associated with the expansion of the sales and professional services staff.
 
    General and Administrative expenses were $863,000 in 1999, compared to
$1,135,000 in 1998. The decrease was due principally to lower costs relating to
investor relations, legal, and information systems consulting.
 
LIQUIDITY AND CAPITAL RESOURCES
 
    Our cash, cash equivalents and marketable securities totaled $7.0 million at
March 31, 1999 compared to $11.9 million at December 31, 1998.
 
    The net cash used in operating activities of $5.2 million in the first
quarter of 1999 reflected the net loss for the quarter of $4.9 million and
prepayments for clinical trials.
 
    We believe that our current cash, cash equivalents, and investments in debt
securities, together with the ability to borrow up to $5 million under a secured
promissory note executed in March 1999, will satisfy our cash requirements at
least through December 31, 1999. Our primary planned uses of cash during that
period are:
 
    - Funding operations;
 
                                       10
<PAGE>
    - Conducting clinical testing of RFS 2000, Nipent-Registered Trademark- and
      product candidates;
 
    - Marketing for expanded indications for Nipent-Registered Trademark- that
      may be developed; and
 
    - Continuing other research and development programs.
 
    Our stock purchase agreement with Tako Ventures, LLC ("Tako"), an investment
entity controlled by Lawrence J. Ellison, a director of the Company, executed in
June 1997, gave Tako certain rights to participate in future sales of common
stock at comparable terms and conditions. In December 1998, we closed a private
placement of common stock to an institutional investor at a 4% discount to a
weighted average stock price prior to the purchase. As a result, in January
1999, Tako exercised its rights and purchased 61,350 shares of unregistered
common stock for a total purchase price of $400,002. We granted Tako
registration rights in connection with this transaction.
 
    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 1999.
 
    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 "Factors Affecting
Future Operating Results."
 
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 $60.8 million from
our inception through March 31, 1999. These losses included non-cash charges of
$7.5 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 $2.7 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
 
                                       11
<PAGE>
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 will require extensive clinical testing before we can
submit any regulatory application for their commercial use.
 
    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 cash, cash equivalents and marketable securities on hand
at March 31, 1999, together with the ability to borrow up to $5 million under a
secured promissory note will be adequate to fund operations and capital
expenditures at least through December 31, 1999. 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.
 
    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 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.
 
                                       12
<PAGE>
    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
and the status of our contingency plans are unchanged from that described in the
1998 annual report.
 
ITEM 3--QUANTITATIVE AND QUALITATIVE DISCLOSURE OF 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.
 
                                       13
<PAGE>
                                 SUPERGEN, INC.
                          PART II - OTHER INFORMATION
 
ITEM 2. CHANGES IN SECURITIES AND USE OF PROCEEDS
 
RECENT SALES OF UNREGISTERED SECURITIES
 
    During the quarter ended March 31, 1999, we issued the following securities:
 
    - 61,350 shares of common stock in January 1999, to Tako Ventures, LLC
      ("Tako"), an investment entity controlled by Lawrence J. Ellison, a
      director of the Company, for $400,002, in connection with Tako's rights to
      participate in a December 1998, private placement of $3,000,000 to an
      institutional investor.
 
    The issuance of shares described above were 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
securities nor were there any other offerees. We relied on representations from
the recipient of the securities 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 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 March
31, 1999, including subsequent exercises of warrants to purchase common stock,
were $23,424,000.
 
    From March 13, 1996, the effective date of the registration statement, to
March 31, 1999, (the Company's fiscal 1999 first 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.............................  16,862,000
Repurchase of common stock.....................................   3,557,000
Purchase of equity investment..................................     500,000
Acquisition of developed technology............................     220,000
</TABLE>
 
                                       14
<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.
 
ITEM 6. EXHIBITS AND REPORTS ON FORM 8-K
 
(a)   Exhibit No.
 
      27.1    Financial Data Schedule--electronic filing only.
 
(b)   During the first quarter of 1999 we filed a Form 8-K dated January 28,
      1999. This Form 8-K described an agreement to acquire Sparta
      Pharmaceuticals, Inc. in exchange for 650,000 shares (subject to
      adjustment) of SuperGen common stock.
 
                                       15
<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> <C>
                                                                              SUPERGEN, INC.
 
Date:                    May 14, 1999                     By:                /s/ JOSEPH RUBINFELD
            --------------------------------------                  --------------------------------------
                                                                           Joseph Rubinfeld, Ph.D.
                                                                     CHIEF EXECUTIVE OFFICER, PRESIDENT,
                                                                      AND DIRECTOR (PRINCIPAL EXECUTIVE
                                                                   OFFICER AND PRINCIPAL FINANCIAL OFFICER)
</TABLE>
 
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