<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0101</schemaVersion>

    <documentType>3</documentType><periodOfReport>2003-07-14</periodOfReport>
    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001252956</issuerCik>
        <issuerName>POLAR MOLECULAR HOLDING CORP</issuerName>
        <issuerTradingSymbol>POMH</issuerTradingSymbol></issuer><reportingOwner><reportingOwnerId>
            <rptOwnerCik>0000943039</rptOwnerCik>
            <rptOwnerName>NELSON MARK L</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>  </rptOwnerStreet1>
            <rptOwnerStreet2>  </rptOwnerStreet2>
            <rptOwnerCity>  </rptOwnerCity>
            <rptOwnerState>  </rptOwnerState>
            <rptOwnerZipCode>  </rptOwnerZipCode>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector><isOfficer>1</isOfficer><isTenPercentOwner>1</isTenPercentOwner><isOther>0</isOther><officerTitle>President/CEO/Chairmn of Bd</officerTitle></reportingOwnerRelationship></reportingOwner><nonDerivativeSecurity><securityTitle><value>Common Stock</value></securityTitle><transactionAmounts><transactionShares><value>5369461</value></transactionShares></transactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value></value></natureOfOwnership></ownershipNature></nonDerivativeSecurity><nonDerivativeSecurity><securityTitle><value>Common Stock</value></securityTitle><transactionAmounts><transactionShares><value>2089233</value></transactionShares></transactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>The Reporting Person disclaims</value><footnoteId id="F1"/></natureOfOwnership></ownershipNature></nonDerivativeSecurity><nonDerivativeSecurity><securityTitle><value>Common Stock</value></securityTitle><transactionAmounts><transactionShares><value>1460356</value></transactionShares></transactionAmounts><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>The Reporting Person disclaims</value><footnoteId id="F2"/></natureOfOwnership></ownershipNature></nonDerivativeSecurity><derivativeSecurity><securityTitle><value>Stock Option (Right to Buy)</value></securityTitle><conversionOrExercisePrice><value>.766</value></conversionOrExercisePrice><exerciseDate><value>1998-02-03</value></exerciseDate><expirationDate><value>2006-12-31</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>65289</value></underlyingSecurityShares></underlyingSecurity><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value></value></natureOfOwnership></ownershipNature></derivativeSecurity><derivativeSecurity><securityTitle><value>Stock Option (Right to Buy)</value></securityTitle><conversionOrExercisePrice><value>1.532</value></conversionOrExercisePrice><exerciseDate><value>1999-02-03</value></exerciseDate><expirationDate><value>2004-02-03</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>196325</value></underlyingSecurityShares></underlyingSecurity><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value></value></natureOfOwnership></ownershipNature></derivativeSecurity><derivativeSecurity><securityTitle><value>Stock Option (Right to Buy)</value></securityTitle><conversionOrExercisePrice><value>1.532</value></conversionOrExercisePrice><exerciseDate><value>1999-02-03</value></exerciseDate><expirationDate><value>2004-02-03</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>233271</value></underlyingSecurityShares></underlyingSecurity><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value></value></natureOfOwnership></ownershipNature></derivativeSecurity><derivativeSecurity><securityTitle><value>Stock Option (Right to Buy)</value></securityTitle><conversionOrExercisePrice><value>1.532</value></conversionOrExercisePrice><exerciseDate><value>1999-02-03</value></exerciseDate><expirationDate><value>2004-02-03</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>429599</value></underlyingSecurityShares></underlyingSecurity><ownershipNature><directOrIndirectOwnership><value>I</value></directOrIndirectOwnership><natureOfOwnership><value>The Reporting Person disclaims </value><footnoteId id="F2"/></natureOfOwnership></ownershipNature></derivativeSecurity><footnotes><footnote id="F1">any pecuniary interest in these shares which are held in a trust in the name of his minor son, David P. Nelson.</footnote><footnote id="F2">any pecuniary interest in these shares which are held in the name of his father, Otis L. Nelson, Jr., who happens to reside with the Reporting Person for more than half of the year.</footnote></footnotes><ownerSignature><signatureName>/S/ Jennifer A. D'Alessandro</signatureName><signatureDate>2003-07-24</signatureDate></ownerSignature></ownershipDocument>

