|CERTIFICATION
PRINCIPAL FINANCIAL OFFICERPURSUANT TO RULE 13a-14(a)


Exhibit 31.2


I, Carter A. Lee, 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/ Carter A. Lee
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Carter A. Lee
Senior Vice President
Finance & Administration
Principal Financial Officer
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