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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2015-04-07</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001488613</issuerCik>
        <issuerName>Foundation Medicine, Inc.</issuerName>
        <issuerTradingSymbol>FMI</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001505781</rptOwnerCik>
            <rptOwnerName>Kleiner Perkins Caufield &amp; Byers XIV, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>2750 SAND HILL ROAD</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>MENLO PARK</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94025</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001546196</rptOwnerCik>
            <rptOwnerName>KPCB XIV Associates, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O KLEINER PERKINS CAUFIELD BYERS</rptOwnerStreet1>
            <rptOwnerStreet2>2750 SAND HILL ROAD</rptOwnerStreet2>
            <rptOwnerCity>MENLO PARK</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94025</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001546197</rptOwnerCik>
            <rptOwnerName>KPCB XIV Founders Fund, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O KLEINER PERKINS CAUFIELD BYERS</rptOwnerStreet1>
            <rptOwnerStreet2>2750 SAND HILL ROAD</rptOwnerStreet2>
            <rptOwnerCity>MENLO PARK</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94025</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>2015-04-07</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>U</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>2100328</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>50.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>502309</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2015-04-07</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>U</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>177684</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>50.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>42495</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F3"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">The amount reported represents the estimated number of shares sold by the reporting person in connection with the tender offer for shares of Common Stock of the Issuer (the &quot;Tender Offer&quot;) by Roche Holdings, Inc. (&quot;Roche&quot;). Roche will purchase only a prorated portion of the shares properly tendered by each tendering stockholder. Based on a preliminary count reported by Roche, the preliminary proration factor for the Tender Offer is approximately 80.7%. If necessary, an amended Form 4 will be filed to report the number of shares actually sold by the reporting person in connection with the Tender Offer once the final proration factor is determined.</footnote>
        <footnote id="F2">The shares are directly held by Kleiner Perkins Caufield &amp; Byers XIV, LLC (&quot;KPCB XIV&quot;). All shares are held for convenience in the name of &quot;KPCB Holdings, Inc., as nominee&quot;. The managing member of KPCB XIV is KPCB XIV Associates, LLC (&quot;XIV Associates&quot;). The voting and dispositive control over the shares is shared by individual managing members of XIV Associates, none of whom has veto power.</footnote>
        <footnote id="F3">The shares are directly held by KPCB XIV Founders Fund, LLC. All shares are held for convenience in the name of &quot;KPCB Holdings, Inc., as nominee&quot;. The managing member of KPCB XIV Founders Fund, LLC is XIV Associates. The voting and dispositive control over the shares is shared by individual managing members of XIV Associates, none of whom has veto power.</footnote>
    </footnotes>

    <remarks>The reporting persons disclaim beneficial ownership of these shares except to the extent of any pecuniary interest therein, and the filing of this report is not an admission that the reporting persons are the beneficial owners of these shares for purposes of Section 16 or for any other purpose.</remarks>

    <ownerSignature>
        <signatureName>/s/ Paul Vronsky as Attorney-In-Fact for Kleiner Perkins Caufield &amp; Byers XIV, LLC</signatureName>
        <signatureDate>2015-04-09</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Paul Vronsky as Attorney-In-Fact for KPCB XIV Associates, LLC</signatureName>
        <signatureDate>2015-04-09</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Paul Vronsky as Attorney-In-Fact for KPCB XIV Founders Fund, LLC</signatureName>
        <signatureDate>2015-04-09</signatureDate>
    </ownerSignature>
</ownershipDocument>
