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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2013-07-23</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001439222</issuerCik>
        <issuerName>AGIOS PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>AGIO</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001508052</rptOwnerCik>
            <rptOwnerName>Flagship Ventures Fund 2007, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE MEMORIAL DRIVE</rptOwnerStreet1>
            <rptOwnerStreet2>7TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001508053</rptOwnerCik>
            <rptOwnerName>Flagship Ventures 2007 General Partner LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE MEMORIAL DRIVE</rptOwnerStreet1>
            <rptOwnerStreet2>7TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001222012</rptOwnerCik>
            <rptOwnerName>AFEYAN NOUBAR</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE MEMORIAL DRIVE</rptOwnerStreet1>
            <rptOwnerStreet2>7TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001255927</rptOwnerCik>
            <rptOwnerName>KANIA EDWIN M JR</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE MEMORIAL DRIVE</rptOwnerStreet1>
            <rptOwnerStreet2>7TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series A Convertible Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F1"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F1"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>3636362</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series C-2 Convertible Preferred Stock</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F3"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>224374</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The Series A Convertible Preferred Stock is convertible into Common Stock on a 1-for-2.75 basis into the number of shares of Common Stock as shown in column 3 at any time at the holder's election and automatically upon the closing of the Issuer's initial public offering.  The shares have no expiration date.</footnote>
        <footnote id="F2">These shares are held by Flagship Ventures Fund 2007, L.P. (&quot;Flagship 2007&quot;).  Flagship Ventures 2007 General Partner, LLC (&quot;Flagship 2007 LLC&quot;) is the general partner of Flagship 2007. Noubar B. Afeyan Ph.D. and Edwin M. Kania, Jr. are the managers of Flagship 2007 LLC. Flagship 2007 LLC and each of these individuals may be deemed to share voting and investment power with respect to all shares held by Flagship 2007. Each of the filing persons disclaims beneficial ownership of the shares except to the extent of any pecuniary interest therein.</footnote>
        <footnote id="F3">The Series C-2 Convertible Preferred Stock is convertible into Common Stock on a 1-for-2.75 basis into the number of shares of Common Stock as shown in column 3 at any time at the holder's election and automatically upon the closing of the Issuer's initial public offering.  The shares have no expiration date.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>By: /s/ Noubar B. Afeyan Ph. D., for Flagship Ventures Fund 2007, L.P. as Manager of Flagship Ventures 2007 General Partner LLC, its General Partner</signatureName>
        <signatureDate>2013-07-23</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>By: /s/ Noubar B. Afeyan Ph. D., as Manager of Flagship Ventures 2007 General Partner LLC</signatureName>
        <signatureDate>2013-07-23</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>By: /s/ Noubar B. Afeyan Ph. D.</signatureName>
        <signatureDate>2013-07-23</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>By: /s/ Edwin M. Kania, Jr.</signatureName>
        <signatureDate>2013-07-23</signatureDate>
    </ownerSignature>
</ownershipDocument>
