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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2019-09-11</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001770787</issuerCik>
        <issuerName>10x Genomics, Inc.</issuerName>
        <issuerTradingSymbol>TXG</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001189140</rptOwnerCik>
            <rptOwnerName>STUELPNAGEL JOHN R</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O 10X GENOMICS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>6230 STONERIDGE MALL ROAD</rptOwnerStreet2>
            <rptOwnerCity>PLEASANTON</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94588</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Class B Common Stock</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>585991</value>
                    <footnoteId id="F2"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Series A-1 Preferred Stock</value>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class A Common Stock</value>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>121686</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series A-2 Preferred Stock</value>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class A Common Stock</value>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>457289</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series B Preferred Stock</value>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class A Common Stock</value>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1253823</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series C Preferred Stock</value>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class A Common Stock</value>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>223304</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Series D Preferred Stock</value>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class A Common Stock</value>
                    <footnoteId id="F3"/>
                    <footnoteId id="F4"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>49634</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F5"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Each share of Class B Common Stock shall be reclassified into one share of Class A Common Stock immediately prior to the completion of the Issuer's initial public offering of Class A Common Stock.</footnote>
        <footnote id="F2">Includes 146,875 shares that are subject to a right of repurchase by the Issuer that lapses over time in accordance with the terms of the stock option awards that were early exercised by the Reporting Person.</footnote>
        <footnote id="F3">Each share of Series A-1 Preferred Stock, Series A-2 Preferred Stock, Series B Preferred Stock, Series C Preferred Stock and Series D Preferred Stock is convertible into shares of Class A Common Stock at any time at the option of the Reporting Person and automatically upon the occurrence of certain other events set forth in the Issuer's Seventh Amended and Restated Certificate of Incorporation on a one-for-one basis and has no expiration date.  Each share of Class A Common Stock is convertible at any time at the option of the Reporting Person into one share of Class B Common Stock and has no expiration date.  Additionally, each share of Class A Common Stock will convert automatically into one share of Class B Common Stock upon transfer, whether or not for value (subject to certain exceptions) and upon the occurrence of certain other events set forth in the Issuer's Seventh Amended and Restated Certificate of Incorporation.</footnote>
        <footnote id="F4">(Continued from Footnote 3) Each share of Class A Common Stock shall be reclassified into one share of Class B Common Stock and each share of Class B Common Stock shall be reclassified into one share of Class A Common Stock immediately prior to the completion of the Issuer's initial public offering of Class A Common Stock.   As a result of this reclassification, each share of Series A-1 Preferred Stock, Series A-2 Preferred Stock, Series B Preferred Stock, Series C Preferred Stock and Series D Preferred Stock shall automatically convert into Class B Common Stock on a one-for-one basis immediately prior to the completion of the Issuer's initial public offering of Class A Common Stock.</footnote>
        <footnote id="F5">These shares are held by the John R. Stuelpnagel Trust, of which the Reporting Person is the sole trustee.</footnote>
    </footnotes>

    <remarks>Exhibit 24 - Power of Attorney</remarks>

    <ownerSignature>
        <signatureName>/s/Eric S. Whitaker, as Attorney-in-Fact</signatureName>
        <signatureDate>2019-09-11</signatureDate>
    </ownerSignature>
</ownershipDocument>
