<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2005-12-23</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0000743884</issuerCik>
        <issuerName>MACROCHEM CORP</issuerName>
        <issuerTradingSymbol>MCMP.OB</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001225978</rptOwnerCik>
            <rptOwnerName>SCO CAPITAL PARTNERS LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1285 AVENUE OF THE AMERICAS</rptOwnerStreet1>
            <rptOwnerStreet2>35TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10019</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001294343</rptOwnerCik>
            <rptOwnerName>Rouhandeh Steven H</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SCO CAPITAL PARTNERS LLC</rptOwnerStreet1>
            <rptOwnerStreet2>1285 AVENUE OF THE AMERICAS, 35TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10019</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series C Cumulative Convertible Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>.175</value>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>11428571</value>
                    <footnoteId id="F1"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Common Stock Purchase Warrants</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>.21</value>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-12-23</value>
            </exerciseDate>
            <expirationDate>
                <value>2011-12-23</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>11428571</value>
                    <footnoteId id="F1"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Placement Agent Warrants</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>.175</value>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-12-23</value>
            </exerciseDate>
            <expirationDate>
                <value>2011-12-23</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1428571</value>
                    <footnoteId id="F1"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By SCO Securities LLC</value>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Amounts reflect adjustment for the 1 for 7 reverse stock split effected by the issuer on December 30, 2005.</footnote>
        <footnote id="F2">This Form 3 is being filed by Steven H. Rouhandeh individually and by SCO Capital Partners LLC, an entity of which Mr. Rouhandeh is the sole member.</footnote>
        <footnote id="F3">SCO Capital Partners LLC is the direct beneficial owner of these securities.</footnote>
        <footnote id="F4">These securities are convertible at any time and have no expiration date.</footnote>
        <footnote id="F5">Mr. Rouhandeh is the sole member of the entity that is the sole member of SCO Securities LLC.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>SCO Capital Partners LLC</signatureName>
        <signatureDate>2006-01-03</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Steven H. Rouhandeh</signatureName>
        <signatureDate>2006-01-03</signatureDate>
    </ownerSignature>
</ownershipDocument>
