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

    <schemaVersion>X0202</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2007-09-19</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001131096</issuerCik>
        <issuerName>ATHENAHEALTH INC</issuerName>
        <issuerTradingSymbol>ATHN</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001412137</rptOwnerCik>
            <rptOwnerName>Nolin Christopher E.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O ATHENAHEALTH, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>311 ARSENAL STREET</rptOwnerStreet2>
            <rptOwnerCity>WATERTOWN</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02472</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Senior VP, GC and Secretary</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>166700</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0.62</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2004-02-06</value>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-02-06</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>20000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.50</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-04-27</value>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2015-04-27</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>5000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>5.26</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2006-02-28</value>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-02-28</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>5000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>7.39</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2007-03-15</value>
                <footnoteId id="F5"/>
            </exerciseDate>
            <expirationDate>
                <value>2017-03-15</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>18000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">These shares are held by the Nolin Investment Trust. Each of Mr. Nolin and his wife are beneficiaries and trustees of such trust, each with independent power as trustee to vote and dispose of all such shares.</footnote>
        <footnote id="F2">100% of the options in this grant were exercisable on the date listed on the table; 60% of the options in this grant vest in equal monthly installments until the third anniversary of the vesting start date of February 1, 2004 and the remaining 40% vest in equal monthly installments until fully vested on the fourth anniversary.</footnote>
        <footnote id="F3">100% of the options in this grant were exercisable on the date listed on the table; 25% of the options vest yearly on the anniversary of the vesting start date of January 9, 2005 until fully vested on the fourth anniversary.</footnote>
        <footnote id="F4">100% of the options in this grant were exercisable on the date listed on the table; 25% of the options vest yearly on the anniversary of the vesting start date of January 9, 2006 until fully vested on the fourth anniversary.</footnote>
        <footnote id="F5">100% of the options in this grant were exercisable on the date listed on the table; 25% of the options vest yearly on the anniversary of the vesting start date of January 1, 2007 until fully vested on the fourth anniversary.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Christopher E. Nolin</signatureName>
        <signatureDate>2007-09-19</signatureDate>
    </ownerSignature>
</ownershipDocument>
