<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>4</documentType><periodOfReport>2003-09-10</periodOfReport>
    <issuer>
        <issuerCik>0001036968</issuerCik>
        <issuerName>VAXGEN INC</issuerName>
        <issuerTradingSymbol>VXGN</issuerTradingSymbol></issuer><reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001217410</rptOwnerCik>
            <rptOwnerName>GURWITH MARC J</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O VAXGEN, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>1000 MARINA BLVD</rptOwnerStreet2>
            <rptOwnerCity>BRISBANE</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94005</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>0</isDirector><isOfficer>1</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther><officerTitle>Senior Vice President</officerTitle></reportingOwnerRelationship></reportingOwner><derivativeTable><derivativeTransaction><securityTitle><value>Incentive Stock Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>5.50</value></conversionOrExercisePrice><transactionDate><value>2003-09-10</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>22721</value></transactionShares><transactionPricePerShare><value>5.50</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2004-09-10</value><footnoteId id="F1"/></exerciseDate><expirationDate><value>2013-09-10</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>22721</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>22721</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></derivativeTransaction><derivativeTransaction><securityTitle><value>Non-Qualified Stock Option (right to buy)</value></securityTitle><conversionOrExercisePrice><value>5.50</value></conversionOrExercisePrice><transactionDate><value>2003-09-10</value></transactionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>22279</value></transactionShares><transactionPricePerShare><value>5.50</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2004-09-10</value><footnoteId id="F1"/></exerciseDate><expirationDate><value>2013-09-10</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>22279</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>22279</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></derivativeTransaction></derivativeTable><footnotes><footnote id="F1">25% of the shares will vest on the first anniversary of the grant date and thereafter, the  remainder will vest in equal monthly installments over the next three years. </footnote></footnotes><remarks/><ownerSignature><signatureName>/s/ Carter A. Lee, Attorney-in-Fact for Marc J. Gurwith</signatureName><signatureDate>2003-12-02</signatureDate></ownerSignature></ownershipDocument>

