<PAGE>

       CERTAIN INFORMATION IN THIS EXHIBIT HAS BEEN OMITTED
       AND FILED SEPARATELY WITH THE COMMISSION. CONFIDENTIAL TREATMENT
       HAS BEEN REQUESTED WITH RESPECT TO THE OMITTED PORTIONS.

                                                                   EXHIBIT 10.9





                      AMENDMENT NO. 1 TO LICENSE AGREEMENT

         This Amendment No. 1 to License Agreement (the "Amendment") is
effective as of March ___, 1996 between KOSAN Biosciences, Inc. ("Licensee") and
THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY ("STANFORD")
concerning the License Agreement between Licensee and STANFORD effective March
11, 1996 (the "Agreement").

1.       Section 1.3 is hereby amended to provide in its entirety as follows:

         LICENSEE desires a license under said Invention(s), Licensed
         Patent(s)and Licensed Materials to develop, manufacture, have made,
         use, and sell Licensed Product(s).

2. Section 14.l is hereby amended to provide in its entirety as follows:

         Licensee may grant sublicenses under the Invention(s), Licensed
Materials and Licensed Patent(s) to make, have made, import, use, lease, sell
and offer for sale and otherwise commercialize and exploit Licensed Products and
Licensed Materials, and practice any method, process or procedure within the
Licensed Patents in the Licensed Territory.

3.       Section 14.3 (a) is hereby amended to provide in its entirety as
         follows:

                  (a) Sublicense terms and conditions shall reflect that any
         sublicensee(s) shall not further sublicense without the written consent
         of STANFORD, which consent shall not be unreasonably withheld;
         provided, however, sublicensees may grant further sublicenses with
         respect to any Licensed Product within the scope of Section 2.5 (ii)
         without the consent of STANFORD;

4.       The last sentence of Section 14.3 is amended to provide in its entirety
         as follows:

         Such sublicenses (including, without limitation, any non-exclusive
         sublicenses) shall remain in effect in the event of any conversion of
         the exclusive license granted herein to a non-exclusive license
         pursuant to Section 3.2 or any termination of this Agreement and shall
         provide for the assignment of such sublicenses to STANFORD or its
         designee, in the event that the Agreement is terminated; provided, the
         financial obligations of each sublicensee to STANFORD shall be limited
         to the amounts Licensee shall be obligated to pay to STANFORD for the
         activities of such sublicensee pursuant to this Agreement.

5. Except as specifically modified or amended hereby, the License Agreement
shall remain in full force and effect and, as so modified or amended, is hereby
ratified, confirmed and approved. No provision of this Amendment may be modified
or amended except expressly in a writing signed by both parties nor shall any
terms be waived except expressly in a writing signed by the party charged
therewith. This Amendment shall be governed in accordance with the laws of the
State of California, without reference to principles of conflicts of laws.



<PAGE>


         IN WITNESS WHEREOF, the parties have duly executed this Amendment as of
the date shown above.

THIE BOARD OF TRUSTEES OF THE                      KOSAN BIOSCIENCES, INC.
THE LELAND STANFORD JUNIOR
UNIVERSITY


By:      /s/ Katharine Ku                          By:       /s/ Daniel V. Santi
    ----------------------------------                 -------------------------

Print Name: Katharine Ku                           Print Name: Daniel V. Santi
           ---------------------------                         -----------------

Title:  DIRECTOR, TECHNOLOGY LICENSING             Title: PRESIDENTE
       -------------------------------                    ----------------------

<PAGE>




KOSAN BIOSCIENCES, INC.
1450 Rollins Road
Burlingame, CA 94010
Tel: 650-343-8673, ext. 207
Fax: 650-343-2931
E-Mail: ostrach@kosan.com

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




September 21, 1998

Ms. Mona Wan
Stanford University
Office of Technology Licensing
900 Welch Road, Suite 3500
Palo Alto, CA 94304

Dear Mona:

This letter will confirm the agreement of Kosan Biosciences, Inc. ("Kosan") and
the Board of Trustees of the Leland Stanford Jr. University ("Stanford") that
Article 11 of the License Agreement entered by Kosan and Stanford effective
March 11, 1996, shall be amended to read in its entirety as follows:

         Prior to the issuance of patents on the Invention(s), LICENSEE agrees
         to use reasonable efforts to mark Licensed Product(s) (or their
         containers or labels) made, sold, or otherwise disposed of by it under
         the license granted in this Agreement with the words "Patent Pending"
         and following the issuance of one or more patents, with the numbers of
         any applicable Licensed Patent(s).

Except as expressly provided above, the Agreement, as amended, shall remain in
full force and effect.


<PAGE>


MS. MONA WAN
SEPTEMBER 21, 1998
PAGE 2




Please indicate Stanford's agreement to the foregoing by having this letter
countersigned below.

Yours sincerely,

/s/ Michael S. Ostrach

Michael S. Ostrach
Vice President, Corporate Development

UNDERSTOOD AND AGREED:

TRUSTEES OF THE LELAND
STANFORD UNIVERSITY


By:  /s/ Katharine Ku
    ----------------------------------------

Name:  KATHARINE KU
     ---------------------------------------

Title: DIRECTOR TECHNOLOGY LICENSING
      --------------------------------------

Date:  Sept. 24, 1998
      --------------------------------------


<PAGE>



                      AMENDMENT NO. 3 TO LICENSE AGREEMENT

This Amendment No. 3 to License Agreement (the "Amendment") is effective as of
March 10, 2000 (the "Effective Date"), between Kosan Biosciences, Inc.
("Licensee") and The Board of Trustees of the Leland Stanford Junior University
("Stanford") and amends the license agreement between Licensee and Stanford
effective March 11,1996, as amended pursuant to that certain Amendment No. 1
effective March 11, 1996, and that certain Amendment No. 2 effective September
21, 1998 (together the "Agreement") for "Recombinant Production of Novel
Polyketides" as described in Stanford Docket S93-098.

WHEREAS,

Licensee has acquired an Exclusive license to the Licensed Patents listed in
Appendix A pursuant to the Agreement;

Stanford owns patent applications claiming technology related to Licensed
Patents, listed in Appendix B;

Both parties anticipate that there may be future inventions from the laboratory
of Dr. Chaitan Khosla that Stanford may offer to add to Appendix B and that
Licensee may wish to license;

Both parties desire to determine the conditions under which the future
inventions may be added to Appendix B and subsequently licensed; and

Stanford and Licensee believe that both parties and the public will benefit by
licensing patent applications listed in Appendix B to Licensee and entering into
this Amendment;

NOW, THEREFORE, Stanford and Licensee agree as follows:

                                SECTION 1 DEFINITIONS

         A.       "Proposed Invention" means a patent application or invention
disclosure that Stanford offers to Licensee for inclusion in Appendix B.
         B. "Optioned Patent" means a Proposed Invention that Licensee agrees to
include in Appendix B, any patent application filed on an invention disclosure
that is a Proposed Invention, and any divisions, continuations, reissues and
foreign counterparts claiming priority to the Proposed Invention.
         C. "New Licensed Patent" means an Optioned Patent for which Licensee
chooses to take an Exclusive license.
         D. "New Non-Exclusive Patent" means an Optioned Patent for which
Licensee chooses to take a non-exclusive license.


                                  Page 1 of 5
<PAGE>


        SECTION 2. GRANT OF OPTION FOR EXCLUSIVE OR NON-EXCLUSIVE LICENSE

Stanford hereby grants Licensee and Licensee hereby accepts an Exclusive option
to acquire an Exclusive or non-exclusive license to Optioned Patents on the
terms and conditions set forth herein If a future patent application or an
invention disclosure: a) names Dr. Chaitan Khosla as an inventor; and b)
describes technology relating to polyketides or the production thereof by
recombinant DNA technology or technology disclosed in Licensed Patents, Stanford
will determine if that patent application or invention disclosure will become a
Proposed Invention. If Stanford decides that a patent application or invention
disclosure will be a Proposed Invention, then Stanford shall provide notice
thereto to Licensee. The Proposed Invention shall be subject to this Amendment

                              SECTION 3 OPTION TERM

The "Option Term" shall begin when Stanford provides notice in writing to
Licensee of the Proposed Invention and shall end EARLIER of:
         a) [**] years after the date Stanford offers the Proposed Invention to
         Licensee in writing; or
         b) [**] after Stanford notifies Licensee in writing that either:
                  i) it has received a Notice of Allowance from the US. Patent
                  and Trademark Office for an Optioned Patent; or ii) a third
                  party has offered or requested licensing terms for the
                  Optioned Patent.

                          SECTION 4 EXERCISE OF OPTION

Licensee may exercise its option at any time during the Option Term by providing
Stanford Written notice of its determination to acquire an Exclusive or
non-exclusive license to the Optioned Patent set forth in such notice. Upon such
notification, the Optioned Patent will become either a New Licensed Patent or a
New Non-Exclusive Patent as appropriate. A New Licensed Patent will be subject
to the terms and conditions of this Amendment and those of any Licensed Patent
in the Agreement. A New Non-Exclusive Patent will be subject to the terms and
conditions of this Amendment and those of any Licensed Patent in the Agreement,
except that:
         a.)      the grant is not Exclusive; and
         b.)      New Non-Exclusive Patent may not be sublicensed.

                                  SECTION 5 PAYMENTS

         A. AMENDMENT OF ISSUE FEE. Within [**] of the Effective Date of this
Amendment No. 3, Licensee shall issue to Stanford shares of Licensee's Series
C preferred stock equivalent to thirty thousand dollars ($30,000).
         B. OPTION FEE. within [**] of the Effective Date of this Amendment
No. 3, Licensee shall pay Stanford [**] dollars ($[**]) as an option fee for
the patent applications listed in Appendix B. To include future

                                  Page 2 of 5


[**] CERTAIN INFORMATION IN THIS EXHIBIT HAS BEEN OMITTED AND FILED SEPARATELY
WITH THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH RESPECT
TO THE OMITTED PORTIONS.

<PAGE>


Proposed Inventions in Appendix B, Licensee shall pay Stanford [**] dollars
($[**]) as the option fee for each Proposed Invention. If a
patent application is filed on a Proposed Invention the option fee shah be paid
by the LATER of: (i) [**] from Stanford's notifying Licensee of a Proposed
Invention; and (ii) [**] from the date a provisional patent application is
filed on a Proposed Invention. If no patent application is filed on a Proposed
Invention the option fee shall be paid by [**] from Stanford's notifying
Licensee of a Proposed Invention. After the option fee is received a Proposed
Invention will become an Optioned Patent. If Licensee does not pay the option
fee, it relinquishes all rights to such Proposed Invention under the Agreement.
Only one such option fee is due for each Proposed Invention.
         C. NON-EXCLUSIVE LICENSE FEE. If Licensee exercises its option by
acquiring a non-exclusive license to an Optioned Patent, then Licensee shall
pay Stanford a non-exclusive license fee of [**] dollars ($[**]) within [**]
of the issuance of the first patent claiming priority to an Optioned Patent.
The non-exclusive license fee is due only one time for each New Non-Exclusive
Patent.
         D. EXCLUSIVE LICENSE FEE. If Licensee decides to exercise its option
to acquire an Exclusive license to an Optioned Patent, then Licensee shall
pay Stanford an Exclusive license fee of [**]dollars ($[**]) within [**] of
the issuance of the first patent claiming priority to such New Licensed
Patent. The amount of the Exclusive license fee shall be determined by
Stanford. Stanford agrees that reductions in the Exclusive license fee (to
not less than [**] dollars ($[**])) may be appropriate when (i) third party
technology licensed to Licensee is used in conjunction with the invention
claimed in the patent; or (ii) the claims of the patent are method claims or
are composition of matter claims that do not encompass the product to be sold
or its method of manufacture. The Exclusive license fee is due only once for
each New Licensed Patent. Licensee may convert a New Licensed Patent to a New
Non-Exclusive Patent upon written notice to Stanford at any time.
         E. ANNUAL FEE FOR PATENTS SUBJECT TO DILIGENCE PLAN. For each New
Licensed Patent subject to a Diligence Plan, as defined in Ss.6, Licensee
shall pay an annual fee of [**] dollars ($[**]). The annual fee is due
beginning on the first [**] after such Diligence Plan is accepted in writing
and every [**] thereafter, for so long as such Diligence Plan is effective.
The amount of the annual fee shall be determined by Stanford. Stanford agrees
that reductions in the fee (to not less than [**] dollars ($[**]) per New
Licensed Patent) may be appropriate when (i) third party technology licensed
to Licensee is used in conjunction with the invention claimed in the patent;
or (ii) the claims of the patent are method claims or are composition of
matter claims that do not encompass the product to be sold or its method of
manufacture. In no event shall the cumulative amount of annual fees due under
this Amendment and annual maintenance fees due under paragraph 6.3 of the
Agreement exceed: [**].
         F. ROYALTIES. For all Optioned Patents, New Non-Exclusive Patents, and
New Licensed Patents, royalties shall be due and payable as set forth in
paragraphs 6.5


                                  Page 3 of 5

[**] CERTAIN INFORMATION IN THIS EXHIBIT HAS BEEN OMITTED AND FILED SEPARATELY
WITH THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH RESPECT
TO THE OMITTED PORTIONS.


<PAGE>


through 6.13 of the Agreement. If a Licensed Product is encompassed by claims
from multiple Licensed Patents, Optioned Patents, New Licensed Patents or New
Non-Exclusive patents, as mended hereby, then Licensee shall pay only one
royalty.

         G. PATENT EXPENSES. Licensee shall pay all patent costs for Optioned
Patents, New Licensed Patents and New Non-Exclusive Patents. Patent costs paid
by Licensee for New Non-Exclusive Patents shall be reimbursable as follows:
         i)       If Stanford licenses the patent to a third party and Licensee
                  submits a written request to Stanford, then Stanford shall
                  reimburse Licensee for [**]% of the past patent costs paid by
                  Licensee.
         ii)      Patent expenses that are not reimbursed are creditable against
                  royalties due under paragraph 6.5 of the Agreement.
         iii)     If Licensee chooses to convert a New Licensed Patent to a New
                  Non-Exclusive Patent, then patent expenses incurred prior to
                  conversion are not reimbursable or creditable.

                            SECTION 6 DILIGENCE PLAN

Licensee shall submit to Stanford a plan (the "Diligence Plan"), acceptable
to Stanford, for developing a New Licensed Patent; such Diligence Plan will
be submitted within [**] of the date Stanford offers a Proposed Invention to
the Licensee in writing. If Licensee does not submit a Diligence Plan or
notifies Stanford in writing that it will no longer adhere to a Diligence
Plan accepted by Stanford, then the New Licensed Patent will be converted to
a New Non-Exclusive Patent.

                             SECTION 7 MISCELLANEOUS

         A. GOOD-STANDING. Stanford and Licensee agree that neither party is
known to be in breach of the Agreement and that both parties are in
good-standing with one another. Both parties agree that prior to this Amendment,
the patents and patent applications licensed to Licensee pursuant to the
Agreement are listed on Appendix A.

         B. LICENSES TO THIRD PARTIES. In the event Stanford licenses a New
Non-Exclusive Patent to a third party, then Stanford shall make good faith
efforts to notify Licensee and to include in such license a statement that the
license does not include rights to Licensed Patents or New Licensed Patents.

         C. RELEASE OF OPTION OR LICENSE. Licensee may release its option or
license rights to a Proposed Invention, Optioned Patent, New Licensed Patent or
New Non-Exclusive Patent at any time by giving Stanford 30 days written notice
of the release. Upon such release, Licensee shall have neither further payment
obligations pursuant to such license other than those previously incurred nor
any rights in such Proposed Invention, Optioned Patent, New Licensed Patent, or
New Non-Exclusive Patent.


                                  Page 4 of 5


[**] CERTAIN INFORMATION IN THIS EXHIBIT HAS BEEN OMITTED AND FILED SEPARATELY
WITH THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH RESPECT
TO THE OMITTED PORTIONS.

<PAGE>


         D. AGREEMENT IN FULL FORCE AND EFFECT. Except as specifically amended
hereby, the Agreement shall remain in full force and effect and as so amended is
hereby ratified, confirmed, and approved. No provision of this Amendment may be
amended except expressly in writing signed by both parties nor shall any terms
be waived except expressly in writing signed by the party charged therewith.
This Amendment shall be governed in accordance with the laws of the State of
California without reference to principles of conflicts of laws.

IN WITNESS WHEREOF, the parties have duly executed this Amendment as of the
Effective Date shown above.

<TABLE>
<S>                                                  <C>
By: /s/ Katherine Ku                                 By: /s/ DANIEL V. SANTI
   ------------------------------------                 -----------------------------------------
Name: KATHERINE KU                                   Daniel V. Santi
     ----------------------------------              President & CEO
Title:   DIRECTOR TECHNOLOGY LICENSING               Date:  15 MAR 00
      ---------------------------------                    --------------------------------------
Date:    Mar 10, 2000
     ----------------------------------
</TABLE>


                                  Page 5 of 5

<PAGE>



                                   APPENDIX A
                                PATENTS LICENSED

<TABLE>
<CAPTION>

<S>                           <C>                    <C>
[**]                          [**]                   [**]

</TABLE>

                            Confidential Information

[**] CERTAIN INFORMATION IN THIS EXHIBIT HAS BEEN OMITTED AND FILED SEPARATELY
WITH THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH RESPECT
TO THE OMITTED PORTIONS.




<PAGE>


[**]

<TABLE>


<S>                              <C>                  <C>
[**]                             [**]                 [**]


</TABLE>

                            Confidential Information


[**] CERTAIN INFORMATION IN THIS EXHIBIT HAS BEEN OMITTED AND FILED SEPARATELY
WITH THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH RESPECT
TO THE OMITTED PORTIONS.




<PAGE>


                                   APPENDIX B
                                PATENTS OPTIONED


<TABLE>


<S>                              <C>                  <C>
[**]                             [**]                 [**]


</TABLE>

                            Confidential Information

[**] CERTAIN INFORMATION IN THIS EXHIBIT HAS BEEN OMITTED AND FILED SEPARATELY
WITH THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH RESPECT
TO THE OMITTED PORTIONS.