|CERTIFICATION CHIEF
EXECUTIVE OFFICERPURSUANT TO RULE 13a-14(a)


Exhibit 31.1


I, Lance K. Gordon, certify that:
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|1. | I have reviewed this quarterly report on Form 10-Q of VaxGen, Inc.
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|2. | Based on my knowledge, this 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 report;
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|3. | Based on my knowledge, the financial statements, and other financial information
          included in this 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 report;
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|4. | The registrants other certifying officer(s) and I are responsible for
          establishing and maintaining disclosure controls and procedures (as defined in
          Exchange Act Rules 13a-15(e) and 15d-15(e)) for the registrant and have:
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| | (a) Designed such disclosure controls and procedures, or caused such disclosure
          controls and procedures to be designed under our supervision, 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 report is being prepared;
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| | (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
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| | (c) Disclosed
in this report any change in the registrants internal control           over
financial reporting that occurred during 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
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|5. | The registrants other certifying officer(s) 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 functions):
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| | (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
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| | (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.
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|November 19, 2003
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|/s/ Lance K. Gordon
Lance K. Gordon, Chief
Executive Officer |  | 
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