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

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2008-06-26</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000824068</issuerCik>
        <issuerName>ATS MEDICAL INC</issuerName>
        <issuerTradingSymbol>ATSI</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001399763</rptOwnerCik>
            <rptOwnerName>Alta Partners VIII, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3700</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001198330</rptOwnerCik>
            <rptOwnerName>NOHRA GUY P</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3700</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001399894</rptOwnerCik>
            <rptOwnerName>Alta Partners Management VIII, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3700</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001198325</rptOwnerCik>
            <rptOwnerName>JANNEY DANIEL</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3700</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001198321</rptOwnerCik>
            <rptOwnerName>CHAMPSI FARAH</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3700</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2008-06-26</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1960000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>1.65</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                    <footnoteId id="F1"/>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>11760000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Warrants</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.65</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2008-06-26</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1960000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>1.65</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2008-05-08</value>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-06-28</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1960000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The purchase of 1,960,000 shares of Common Stock was made by Alta Partners VIII, LP (&quot;APVIII&quot;) through the exercise of warrants.</footnote>
        <footnote id="F2">These securities and warrants are held by APVIII.  Alta Partners Management VIII, LLC (&quot;APMVIII&quot;) is the general partner of APVIII.  Guy Nohra, Daniel Janney, and Farah Champsi are managing directors of APMVIII and excercise shared voting and investment power with respect to the shares owned by APVIII.  Each of the reporting persons disclaims beneficial ownership of such securities, except to the extent of his or its proportionate pecuniary interest herein.  Mr. Nohra is a director of the Issuer.</footnote>
        <footnote id="F3">As decribed in previous filings by the reporting person, upon receipt of shareholder approval on May 8, 2008, the initial exercise date of the warrant became May 8, 2008 instead of June 28, 2008, and the warrant became a right to acquire shares of common stock instead of cash.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>By Alta Partners Management VIII, LLC, by /s/ Guy Nohra, Managing Director</signatureName>
        <signatureDate>2008-06-30</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Guy Nohra</signatureName>
        <signatureDate>2008-06-30</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Guy Nohra, Managing Director</signatureName>
        <signatureDate>2008-06-30</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Daniel Janney</signatureName>
        <signatureDate>2008-06-30</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Farah Champsi</signatureName>
        <signatureDate>2008-06-30</signatureDate>
    </ownerSignature>
</ownershipDocument>
