EXHIBIT 31.1



CERTIFICATION



I, Daniel V. Santi, M.D., Ph.D., Chief Executive Officer of Kosan Biosciences Incorporated, certify that:



1. I have reviewed this Quarterly Report on Form 10-Q of Kosan Biosciences
Incorporated;



2. Based on my knowledge, this Quarterly Report
does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered
by this Quarterly Report;



3. Based on my knowledge, the
financial statements, and other financial information included in this Quarterly Report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in
this Quarterly Report;



4. The registrants other
certifying officers and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-14 and 15d-14) for the registrant and we have:



a) Designed such disclosure controls and procedures to ensure that material
information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this Quarterly Report is being prepared;



b) Evaluated the effectiveness of the registrants disclosure controls
and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and



c) Disclosed in this report any change in the registrants internal
control over financial reporting that occurred during the registrants most recent fiscal quarter (the registrants fourth quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect,
the registrants internal control over financial reporting; and



5. The registrants other certifying officers and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrants auditors and the audit committee of registrants board
of directors (or persons performing the equivalent function):



a) All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrants ability to record, process, summarize and
report financial information; and



b) Any fraud, whether or not
material, that involves management or other employees who have a significant role in the registrants internal control over financial reporting.



6. The registrants other certifying officers and I have indicated in this Quarterly Report whether or not there were significant changes in internal
controls or in other factors that could significantly affect internal controls subsequent to the date of our most recent evaluation, including any corrective actions with regard to significant deficiencies and material weaknesses.



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|Date: May 7, 2004 |  |  |  | By: |  | /s/ Daniel V. Santi, M.D., Ph.D.
|                  |  |  |  |     |  |                                  | 
|                  |  |  |  |     |  |                                  |  | Daniel V. Santi, M.D., Ph.D. Chairman and Chief Executive Officer