Exhibit 31.1 CERTIFICATION OF CHIEF EXECUTIVE OFFICER I, James P. Panek, certify that: 1.
I have reviewed this quarterly report on Form 10-Q of
  VaxGen, Inc.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;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;4.
The registrants other certifying officer 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)) and
  internal control over financial reporting (as defined in Exchange Act Rules
  13a-15(f) and 15d-15(f)) for the registrant and have:(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;(b) Designed such internal control over financial
  reporting, or caused such internal control over financial reporting to be
  designed under our supervision, to provide reasonable assurance regarding the
  reliability of financial reporting and the preparation of financial
  statements for external purposes in accordance with generally accepted
  accounting principles;(c) 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(d) 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; and5.
The registrants other certifying officer 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):(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. May 30, 2007 /s/ James P. Panek Chief Executive Officer 1