|CERTIFICATION CHIEF EXECUTIVE OFFICER
PURSUANT 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/A 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


/s/ Lance K. Gordon
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Lance K. Gordon, Chief Executive Officer
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