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

    <documentType>4</documentType><periodOfReport>2003-05-15</periodOfReport>
    <issuer>
        <issuerCik>0000779164</issuerCik>
        <issuerName>PROTERION CORP</issuerName>
        <issuerTradingSymbol>PRC</issuerTradingSymbol></issuer><reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001241687</rptOwnerCik>
            <rptOwnerName>PRUDHOMME ROBERT K</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE POSSUMTOWN ROAD</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>PISCATAWAY</rptOwnerCity>
            <rptOwnerState>NJ</rptOwnerState>
            <rptOwnerZipCode>08854</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
            <reportingOwnerRelationship>
<isDirector>1</isDirector><isOfficer>0</isOfficer><isTenPercentOwner>0</isTenPercentOwner><isOther>0</isOther></reportingOwnerRelationship></reportingOwner><derivativeTable><derivativeTransaction><securityTitle><value>Option (right to buy)</value><footnoteId id="F1"/></securityTitle><conversionOrExercisePrice><value>.31</value></conversionOrExercisePrice><transactionDate><value>2003-05-15</value></transactionDate><deemedExecutionDate><value>1988-08-08</value></deemedExecutionDate><transactionCoding><transactionFormType>4</transactionFormType><transactionCode>A</transactionCode><equitySwapInvolved>0</equitySwapInvolved></transactionCoding><transactionAmounts><transactionShares><value>40000</value></transactionShares><transactionPricePerShare><value>0</value></transactionPricePerShare><transactionAcquiredDisposedCode><value>A</value></transactionAcquiredDisposedCode></transactionAmounts><exerciseDate><value>2003-11-15</value><footnoteId id="F2"/></exerciseDate><expirationDate><value>2013-05-15</value></expirationDate><underlyingSecurity><underlyingSecurityTitle><value>Common Stock</value></underlyingSecurityTitle><underlyingSecurityShares><value>40000</value></underlyingSecurityShares></underlyingSecurity><postTransactionAmounts><sharesOwnedFollowingTransaction><value>40000</value></sharesOwnedFollowingTransaction></postTransactionAmounts><ownershipNature><directOrIndirectOwnership><value>D</value></directOrIndirectOwnership><natureOfOwnership><value/></natureOfOwnership></ownershipNature></derivativeTransaction></derivativeTable><footnotes><footnote id="F1">Option to purchase shares under the Company's 2003 Equity Incentive Plan.</footnote><footnote id="F2">The option vests in twelve equal monthly installments beginning on June 18, 2003, however, the vested portion is not first exercisable until six months after May 15, 2003.</footnote></footnotes><remarks/><ownerSignature><signatureName>ROBERT K. PRUD'HOMME</signatureName><signatureDate>2003-06-15</signatureDate></ownerSignature></ownershipDocument>

