<PAGE>

                                                         Exhibit 10.29

                                              CONFIDENTIAL TREATMENT REQUEST

*Portions denoted with an asterisk have been omitted and filed separately 
with the Securities and Exchange Commission pursuant to a request for 
confidential treatment.


                            REGISTRATION RIGHTS AGREEMENT

               THIS REGISTRATION RIGHTS AGREEMENT, dated as of November 23, 1998
(this "Agreement"), is made by and between SUPERGEN, INC., a Delaware
corporation (the "Company"), and * (the "Investor").

                                 W I T N E S S E T H:

               WHEREAS, upon the terms and subject to the conditions of the
Common Stock Purchase Agreement, dated as of November 23, 1998, between the
Investor and the Company (the "Purchase Agreement"), the Company has agreed to
issue and sell to the Investor, in an amount up to $3,000,000, shares of the
common stock, $.0001 par value per share (the "Common Stock"), of the Company
(the "Shares"); and 

               WHEREAS, to induce the Investor to execute and deliver the
Purchase Agreement, the Company has agreed to provide certain registration
rights under the Securities Act of 1933, as amended, and the rules and
regulations thereunder, or any similar successor statute (collectively, the
"Securities Act"), with respect to the Shares and Warrant Shares;

               NOW, THEREFORE, in consideration of the premises and the mutual
covenants contained herein and other good and valuable consideration, the
receipt and sufficiency of which are hereby acknowledged, the Company and the
Investor hereby agrees as follows:

               1.     DEFINITIONS.

               (a)    As used in this Agreement, the following terms shall have
the following meanings:

               (i)    "Investor" means the Investor and any permitted
transferee or assignee who agrees to become bound by the provisions of this
Agreement in accordance with Section 9 hereof.

               (ii)   "Register," "Registered," and "Registration" refer to a
registration effected by preparing and filing a Registration Statement or
Statements in compliance with the Securities Act and pursuant to Rule 415 under
the Securities Act or any successor rule providing for offering securities on a
continuous basis ("Rule 415"), and the declaration or ordering of effectiveness
of such Registration Statement by the United States Securities and Exchange
Commission (the "SEC").

               (iii)  "Registrable Securities" means the Shares.

                                         -1-
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                                                  CONFIDENTIAL TREATMENT REQUEST

               (iv)   "Registration Statement" means a registration statement
of the Company under the Securities Act.

               (b)    Capitalized terms used herein and not otherwise defined
herein shall have the respective meanings set forth in the Purchase Agreement.

               2.     REGISTRATION.

               (a)    MANDATORY REGISTRATION.  The Company shall prepare and
file with the SEC a Registration Statement on an appropriate form for
registering for resale by the Investor the Shares and the Company shall use its
best efforts to cause the Registration Statement to be declared effective no
later than 75 days after the Closing Date.  

               (b)    PAYMENTS BY THE COMPANY.  

                      If the Registration Statement covering the Registrable
Securities required to be filed by the Company pursuant to Section 2(a) hereof
(i) has not been filed within thirty (30) days from the Closing Date, the
Company will pay the Investor liquidated damages equal to $20,000 per month for
each month (pro rated for a period which is less than an entire month) that the
Company fails to file the Registration Statement and/or (ii) has not been
declared effective by seventy-five (75) days following the Closing Date (except
as provided by the last sentence of Section 2(a)), then the Company will pay the
Investor liquidated damages equal to $20,000 per month for each month (pro rated
for a period which is less than an entire month) until the earlier of (x) the
date such Registration Statement is declared effective or (y) the date all such
Registrable Securities may be sold in reliance on Rule 144.

               3.     OBLIGATIONS OF THE COMPANY.  In connection with the
registration of the Registrable Securities, the Company shall do each of the
following.

               (a)    Prepare promptly and file with the SEC, a Registration
Statement with respect to not less than the number of Registrable Securities
provided in Section 2(a), above, and thereafter use its best efforts to cause
each Registration Statement relating to Registrable Securities to become
effective seventy-five (75) days after the Closing Date, and keep the
Registration Statement effective at all times until the earliest (the
"Registration Period") of (i) the date that is three years after the Closing
Date (ii) the date when the Investor may sell all Registrable Securities under
Rule 144 or (iii) the date the Investor no longer owns any of the Registrable
Securities, which Registration Statement (including any amendments or
supplements thereto and prospectuses contained therein) shall not contain any
untrue statement of a material fact or omit to state a material fact required to
be stated therein or necessary to make the statements therein, in light of the
circumstances in which they were made, not misleading;

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                                                  CONFIDENTIAL TREATMENT REQUEST

               (b)    Prepare and file with the SEC such amendments (including
post-effective amendments) and supplements to the Registration Statement and the
prospectus used in connection with the Registration Statement as may be
necessary to keep the Registration Statement effective at all times during the
Registration Period, and, during the Registration Period, comply with the
provisions of the Securities Act with respect to the disposition of all
Registrable Securities of the Company covered by the Registration Statement
until such time as all of such Registrable Securities have been disposed of in
accordance with the intended methods of disposition by the seller or sellers
thereof as set forth in the Registration Statement;

               (c)    The Company shall permit a single firm of counsel
designated by the Investor to review the Registration Statement and all
amendments and supplements thereto a reasonable period of time prior to their
filing with the SEC;

               (d)    Furnish to the Investor whose Registrable Securities are
included in the Registration Statement and its legal counsel identified to the
Company, (i) promptly after the same is prepared and publicly distributed, filed
with the SEC, or received by the Company, one (1) copy of the Registration
Statement, each preliminary prospectus and prospectus, and each amendment or
supplement thereto, and (ii) such number of copies of a prospectus, and all
amendments and supplements thereto and such other documents, as the Investor may
reasonably request in order to facilitate the disposition of the Registrable
Securities owned by the Investor;

               (e)    As promptly as practicable after becoming aware of such
event, the Company shall notify the Investor of (x) the issuance by the SEC of a
stop order suspending the effectiveness of the Registration Statement, (y) the
happening of any event of which the Company has knowledge as a result of which
the prospectus included in the Registration Statement, as then in effect,
includes an untrue statement of a material fact or omits to state a material
fact required to be stated therein or necessary to make the statements therein,
in light of the circumstances under which they were made, not misleading, or (z)
the occurrence or existence of any pending corporate development that, in the
reasonable discretion of the Company, makes it appropriate to suspend the
availability of the Registration Statement, and use its best efforts promptly to
prepare a supplement or amendment to the Registration Statement to correct such
untrue statement or omission, and deliver such number of copies of such
supplement or amendment to each Investor as such Investor may reasonably
request; provided that, for not more than twenty (20) days (or a total of not
more than forty (40) days in any twelve (12) month period, the Company may delay
the disclosure of material non-public information concerning the Company (as
well as prospectus or Registration Statement updating) the disclosure of which
at the time is not, in the good faith opinion of the Company, the best interests
of the Company and in the opinion of counsel to the Company (an "Allowed
Delay"); provided, further, that the Company shall promptly (i) notify the
Investor in writing of the existence of material non-public information giving
rise to an Allowed Delay and (ii) advise the Investor in writing to cease all
sales under the Registration Statement until the end of the Allowed Delay.  Upon
expiration of the Allowed Delay, the Company shall again be bound by the first
sentence of this Section 3(f) 

                                       -3-
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                                                  CONFIDENTIAL TREATMENT REQUEST

with respect to the information giving rise thereto, and shall be obligated 
to pay to the Investors any amounts provided for in Section 2(b).

               (f)    As promptly as practicable after becoming aware of such
event, notify the Investor who holds Registrable Securities being sold (or, in
the event of an underwritten offering, the managing underwriters) of the
issuance by the SEC of a Notice of Effectiveness or any notice of effectiveness
or any stop order or other suspension of the effectiveness of the Registration
Statement at the earliest possible time;

               (g)    Provide a transfer agent and registrar, which may be a
single entity, for the Registrable Securities not later than the effective date
of the Registration Statement;

               (h)    Cooperate with the Investor who hold Registrable
Securities being offered to facilitate the timely preparation and delivery of
certificates for the Registrable Securities to be offered pursuant to the
Registration Statement and enable such certificates for the Registrable
Securities to be in such denominations or amounts as the case may be, as the
Investor may reasonably request, and, within three (3) business days after a
Registration Statement which includes Registrable Securities is ordered
effective by the SEC, the Company shall deliver, and shall cause legal counsel
selected by the Company to deliver, to the transfer agent for the Registrable
Securities (with copies to the Investor whose Registrable Securities are
included in such Registration Statement) an appropriate instruction and opinion
of such counsel; and

               (i)    Take all other reasonable actions necessary to expedite
and facilitate disposition by the Investor of the Registrable Securities
pursuant to the Registration Statement.

               4.     OBLIGATIONS OF THE INVESTOR.  In connection with the
registration of the Registrable Securities, the Investor shall have the
following obligations:

               (a)    It shall be a condition precedent to the obligations of
the Company to complete the registration pursuant to this Agreement with respect
to the Registrable Securities of the Investor that the Investor shall furnish to
the Company such information regarding itself, the Registrable Securities held
by it, and the intended method of disposition of the Registrable Securities held
by it, as shall be reasonably required to effect the registration of such
Registrable Securities and shall execute such documents in connection with such
registration as the Company may reasonably request.  At least five (5) days
prior to the first anticipated filing date of the Registration Statement, the
Company shall notify the Investor of the information the Company requires from
the Investor (the "Requested Information").

               (b)    The Investor agrees to cooperate with the Company as
reasonably requested by the Company in connection with the preparation and
filing of the Registration Statement hereunder; and

                                       -4-
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                                                  CONFIDENTIAL TREATMENT REQUEST

               (c)    The Investor agrees that, upon receipt of any notice from
the Company of the happening of any event of the kind described in Section 3(e)
or 3(f), above, the Investor will immediately discontinue disposition of
Registrable Securities pursuant to the Registration Statement covering such
Registrable Securities until the Investor's receipt of the copies of the
supplemented or amended prospectus contemplated by Section 3(e) or 3(f) and, if
so directed by the Company, the Investor shall deliver to the Company (at the
expense of the Company) or destroy (and deliver to the Company a certificate of
destruction) all copies in the Investor's possession, of the prospectus covering
such Registrable Securities current at the time of receipt of such notice.

               5.     EXPENSES OF REGISTRATION.  All reasonable expenses, other
than underwriting discounts and commissions incurred in connection with
registrations, filings or qualifications pursuant to Section 3, but including,
without limitation, all registration, listing, and qualifications fees, printers
and accounting fees, the fees and disbursements of counsel for the Company,
shall be borne by the Company.

               6.     INDEMNIFICATION.  The rights of the Investor and the
Company to indemnification and/or contribution in the event any Registrable
Securities are included in a Registration Statement under this Agreement are set
forth on Schedule A hereto.

               7.     REPORTS UNDER EXCHANGE ACT.  With a view to making
available to the Investor the benefits of Rule 144 promulgated under the
Securities Act or any other similar rule or regulation of the SEC that may at
any time permit the Investor to sell securities of the Company to the public
without registration ("Rule 144"), the Company agrees to:

               (a)    make and keep public information available, as those
terms are understood and defined in Rule 144;

               (b)    file with the SEC in a timely manner all reports and
other documents required of the Company under the Securities Act and the
Exchange Act; and

               (c)    furnish to the Investor so long as the Investor owns
Registrable Securities, promptly upon request, (i) a written statement by the
Company that it has complied with the reporting requirements of Rule 144, the
Securities Act and the Exchange Act, (ii) a copy of the most recent annual or
quarterly report of the Company and such other reports and documents so filed by
the Company and (iii) such other information as may be reasonably requested to
permit the Investor to sell such securities pursuant to Rule 144 without
registration.

               8.     ASSIGNMENT OF THE REGISTRATION RIGHTS.  The rights to
have the Company register Registrable Securities pursuant to this Agreement
shall be automatically assigned by the Investor to any transferee of the
Registrable Securities only if:  (a) the Investor agrees in writing with the
transferee or assignee to assign such rights, and a copy of such agreement is
furnished to 

                                       -5-

<PAGE>
                                                  CONFIDENTIAL TREATMENT REQUEST

the Company within a reasonable time after such assignment, (b) the Company 
is, within a reasonable time after such transfer or assignment, furnished 
with written notice of (i) the name and address of such transferee or 
assignee and (ii) the securities with respect to which such registration 
rights are being transferred or assigned, (c) immediately following such 
transfer or assignment the further disposition of such securities by the 
transferee or assignee is restricted under the Securities Act and applicable 
state securities laws, (d) at or before the time the Company received the 
written notice contemplated by clause (b) of this sentence the transferee or 
assignee agrees in writing with the Company to be bound by all of the 
provisions contained herein, and (e) such transferee shall be an "accredited 
investor" as defined in Rule 501 of Regulation D.  In the event of any delay 
in filing or effectiveness of the Registration Statement as a result of such 
assignment, the Company shall not be liable for any damages arising from such 
delay, or the payments set forth in Section 2(b) hereof.

               9.     AMENDMENT OF REGISTRATION RIGHTS.  Any provision of this
Agreement may be amended and the observance thereof may be waived (either
generally or in a particular instance and either retroactively or
prospectively), only with the written consent of the Company and the Investor. 
Any amendment or waiver effected in accordance with this Section 9 shall be
binding upon the Investor and the Company.

               10.    MISCELLANEOUS.

               (a)    A person or entity is deemed to be a holder of
Registrable Securities whenever such person or entity owns of record such
Registrable Securities.  If the Company receives conflicting instructions,
notices or elections from two or more persons or entities with respect to the
same Registrable Securities, the Company shall act upon the basis of
instructions, notice or election received from the registered owner of such
Registrable Securities.

               (b)    Notices required or permitted to be given hereunder shall
be in writing and shall be deemed to be sufficiently given when personally
delivered (by hand, by courier, by telephone line facsimile transmission,
receipt confirmed, or other means) or sent by certified mail, return receipt
requested, properly addressed and with proper postage pre-paid (i) if to the
Company, 2 Annabel Lane, Suite 220, San Ramon, California  94583, Attention: 
Joseph Rubinfeld, with a copy to Wilson Sonsini Goodrich & Rosati, 650 Page Mill
Road, Palo Alto, California  94304-1050, Attention:  Kathleen Block, Esq.; and
(ii) if to the Investor, at *, or at such other address as each such party
furnishes by notice given in accordance with this Section 10(b), and shall be
effective, when personally delivered, upon receipt and, when so sent by
certified mail, four (4) calendar days after deposit with the United States
Postal Service.

               (c)    Failure of any party to exercise any right or remedy
under this Agreement or otherwise, or delay by a party in exercising such right
or remedy, shall not operate as a waiver thereof.

                                       -6-
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                                                  CONFIDENTIAL TREATMENT REQUEST

               (d)    This Agreement shall be governed by and interpreted in
accordance with the internal laws of the State of Delaware, without giving
effect to the choice of law provisions.  Each of the Company and the Investor
(i) hereby irrevocably submits to the jurisdiction of the United States District
Court and other courts of the United States sitting in the State of Delaware for
the purposes of any suit, action or proceeding arising out of or relating to
this Agreement and (ii) hereby waives, and agrees not to assert in any such
suit, action or proceeding, any claim that it is not personally subject to the
jurisdiction of such court, that the suit, action or proceeding is brought in an
inconvenient forum or that the venue of the suit, action or proceeding is
improper.  Each of the Company and the Investor consents to process being served
in any such suit, action or proceeding by mailing a copy thereof to such party
at the address in effect for notices to it under this Agreement and agrees that
such service shall constitute good and sufficient service of process and notice
thereof.  Nothing in this Section shall affect or limit any right to serve
process in any other manner permitted by law.

               (e)    A facsimile transmission of this signed Agreement shall
be legal and binding on all parties hereto.  If any provision of this Agreement
shall be invalid or unenforceable in any jurisdiction, such invalidity or
unenforceability shall not affect the validity or enforceability of the
remainder of this Agreement or the validity or enforceability of this Agreement
in any other jurisdiction.  This Agreement may be amended only by an instrument
in writing signed by the party to be charged with enforcement.  This Agreement
supersedes all prior agreements and understandings among the parties hereto with
respect to the subject matter hereof.  

               (f)    This Agreement and the Purchase Agreement constitute the
entire agreement among the parties hereto with respect to the subject matter
hereof and supercede all prior agreements with respect to the subject matter
hereof.  There are no restrictions, promises, warranties or undertakings, other
than those set forth or referred to herein.  This Agreement supersedes all prior
agreements and understandings among the parties hereto with respect to the
subject matter hereof.

               (g)    Subject to the requirements of Section 8 hereof, this
Agreement shall inure to the benefit of and be binding upon the successors and
assigns of each of the parties hereto.

               (h)    All pronouns and any variations thereof refer to the
masculine, feminine or neuter, singular or plural, as the context may require.

               (i)    The headings in this Agreement are for convenience of
reference only and shall not limit or otherwise affect the meaning thereof.

               (i)    This Agreement may be executed in two or more
counterparts, each of which shall be deemed an original but all of which shall
constitute one and the same agreement.  This Agreement, once executed by a
party, may be delivered to the other party hereto by 

                                       -7-
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                                                  CONFIDENTIAL TREATMENT REQUEST

telephone line facsimile transmission of a copy of this Agreement bearing the 
signature of the party so delivering this Agreement.

               (j)    Neither party shall be liable for consequential damages.

               IN WITNESS WHEREOF, the parties have caused this Agreement to be
duly executed by their respective officers thereunto duly authorized as of the
day and year first above written.


                                             SUPERGEN, INC.


                                             By: /s/ Dr. Joseph Rubinfeld     
                                                ------------------------------
                                                Name: Dr. Joseph Rubinfeld 
                                                Title: Chief Executive Officer



                                             *


                                             By:  /s/ *   
                                                ------------------------------
                                                Name:  *
                                                Title: *



                                       -8-
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                                                  CONFIDENTIAL TREATMENT REQUEST

                                      SCHEDULE A

          (a)  To the extent permitted by law, the Company will
indemnify and hold harmless the Investor who holds such Registrable Securities,
the directors, if any, of the Investor, the officers, if any, of the Investor,
each person, if any, who controls the Investor within the meaning of the
Securities Act or the Exchange Act (each, an "Indemnified Person" or
"Indemnified Party"), against any losses, claims, damages, liabilities or
reasonable expenses (joint or several) incurred (collectively, "Claims") to
which any of them may become subject under the Securities Act, the Exchange Act
or otherwise, insofar as such Claims (or actions or proceedings, whether
commenced or threatened, in respect thereof) arise out of or are based upon any
of the following statements, omissions or violations in the Registration
Statement, or any post-effective amendment thereof, or any prospectus included
therein: (i) any untrue statement or alleged untrue statement of a material fact
contained in the Registration Statement or any post-effective amendment thereof
or the omission or alleged omission to state therein a material fact required to
be stated therein or necessary to make the statements therein not misleading,
(ii) any untrue statement or alleged untrue statement of a material fact
contained in the final prospectus (as amended or supplemented, if the Company
files any amendment thereof or supplement thereto with the SEC) or the omission
or alleged omission to state therein any material fact necessary to make the
statements made therein, in light of the circumstances under which the
statements therein were made, not misleading or (iii) any violation or alleged
violation by the Company of the Securities Act, the Exchange Act, any state
securities law or any rule or regulation under the Securities Act, the Exchange
Act or any state securities law (the matters in the foregoing clauses (i)
through (iii) being, collectively, "Violations").  Subject to clause (b) of this
Schedule A, the Company shall reimburse the Investor, promptly as such expenses
are incurred and are due and payable, for any reasonable legal fees or other
reasonable expenses incurred by them in connection with investigating or
defending any such Claim.  Notwithstanding anything to the contrary contained
herein, the indemnification agreement contained in this clause (a) shall not (I)
apply to a Claim arising out of or based upon a Violation which occurs in
reliance upon and in conformity with information furnished in writing to the
Company by or on behalf of any Indemnified Person expressly for use in
connection with the preparation of the Registration Statement or any such
amendment thereof or supplement thereto, (II) be available to the extent such
Claim is based on a failure of the Investor to deliver or cause to be delivered
the prospectus made available by the Company; or (III) apply to amounts paid in
settlement of any Claim if such settlement is effected without the prior written
consent of the Company, which consent shall not be unreasonably withheld.  The
Investor ill indemnify the Company and its officers, directors and agents and
each person, if any, who controls the Company within the meaning of the
Securities Act or the Exchange Act against any Claims arising out of or based
upon a Violation which occurs in reliance upon and in conformity with
information furnished in writing to the Company, by or on behalf of the
Investor, expressly for use in connection with the preparation of the
Registration Statement, subject to such limitations and conditions as are
applicable to the Indemnification provided by the Company hereunder.  

                                       A-1-
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                                                  CONFIDENTIAL TREATMENT REQUEST

Such indemnity shall remain in full force and effect regardless of any 
investigation made by or on behalf of the Indemnified Person and shall 
survive the transfer of the Registrable Securities by the Investor pursuant 
to Section 8 of this Agreement.

          (b)  Promptly after receipt by an Indemnified Person or
Indemnified Party under this Schedule A of notice of the commencement of any
action (including any governmental action), such Indemnified Person or
Indemnified Party shall, if a Claim in respect thereof is to be made against any
indemnifying party under this Schedule A, deliver to the indemnifying party a
written notice of the commencement thereof and the indemnifying party shall have
the right to participate in, and, to the extent the indemnifying party so
desires, jointly with any other indemnifying party similarly noticed, to assume
control of the defense thereof with counsel mutually satisfactory to the
indemnifying party and the Indemnified Person or the Indemnified Party, as the
case may be.  In case any such action is brought against any Indemnified Person
or Indemnified Party, and it notifies the indemnifying party of the commencement
thereof, the indemnifying party will be entitled to participate in, and, to the
extent that it may wish, jointly with any other indemnifying party similarly
notified, assume the defense thereof, subject to the provisions herein stated
and after notice from the indemnifying party to such Indemnified Person or
Indemnified Party of its election so to assume the defense thereof, the
indemnifying party will not be liable to such Indemnified Person or Indemnified
Party under this Schedule A for any legal or other reasonable out-of-pocket
expenses subsequently incurred by such Indemnified Person or Indemnified Party
in connection with the defense thereof other than reasonable costs of
investigation, unless the indemnifying party shall not pursue the action of its
final conclusion.  The Indemnified Person or Indemnified Party shall have the
right to employ separate counsel in any such action and to participate in the
defense thereof, but the reasonable fees and reasonable out-of-pocket expenses
of such counsel shall not be at the expense of the indemnifying party if the
indemnifying party has assumed the defense of the action with counsel reasonably
satisfactory to the Indemnified Person or Indemnified Party.  The failure to
deliver written notice to the indemnifying party within a reasonable time of the
commencement of any such action shall not relieve such indemnifying party of any
liability to the Indemnified Person or Indemnified Party under this Schedule A,
except to the extent that the indemnifying party is prejudiced in its ability to
defend such action.  The indemnification required by this Schedule A shall be
made by periodic payments of the amount thereof during the course of the
investigation or defense, as such expense, loss, damage or liability is incurred
and is due and payable.

          (c)  To the extent any indemnification by an indemnifying party is 
prohibited or limited by law, the indemnifying party agrees to make the 
maximum contribution with respect to any amounts for which it would otherwise 
be liable under this Schedule A to the fullest extent permitted by law; 
PROVIDED, HOWEVER, that (a) no contribution shall be made under circumstances 
where the maker would not have been liable for indemnification under the 
fault standards set forth in this Schedule A; (b) no seller of Registrable 
Securities guilty of fraudulent misrepresentation (within the meaning of 
Section 11(f) of the Securities Act) shall be entitled to contribution from 
any seller of Registrable Securities who was not guilty of such fraudulent 

                                         A-2-
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                                                  CONFIDENTIAL TREATMENT REQUEST

misrepresentation; and (c) contribution by any seller of Registrable 
Securities shall be limited in amount to the net amount of proceeds received 
by such seller from the sale of such Registrable Securities.

                                       A-3-