<?xml version="1.0" encoding="utf-8"?>
<!--XBRL document created by Certent Disclosure Management 6.37.3.1 -->
<!--Based on XBRL 2.1-->
<!--Created on: 8/6/2020 1:09:16 PM-->
<!--Modified on: 8/6/2020 1:09:16 PM-->
<linkbase xmlns="http://www.xbrl.org/2003/linkbase" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xlink="http://www.w3.org/1999/xlink" xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd">
  <roleRef xlink:type="simple" xlink:href="pacb-20200630.xsd#StatementCondensedConsolidatedBalanceSheets" roleURI="http://www.pacificbiosciences.com/role/StatementCondensedConsolidatedBalanceSheets"></roleRef>
  <roleRef xlink:type="simple" xlink:href="pacb-20200630.xsd#StatementCondensedConsolidatedStatementsOfOperationsAndComprehensiveLoss" roleURI="http://www.pacificbiosciences.com/role/StatementCondensedConsolidatedStatementsOfOperationsAndComprehensiveLoss"></roleRef>
  <roleRef xlink:type="simple" xlink:href="pacb-20200630.xsd#StatementCondensedConsolidatedStatementsOfCashFlows" roleURI="http://www.pacificbiosciences.com/role/StatementCondensedConsolidatedStatementsOfCashFlows"></roleRef>
  <roleRef xlink:type="simple" xlink:href="pacb-20200630.xsd#DisclosureSummaryOfSignificantAccountingPoliciesSummaryOfAssetsAndLiabilitiesMeasuredAtFairValueOnRecurringBasisDetails" roleURI="http://www.pacificbiosciences.com/role/DisclosureSummaryOfSignificantAccountingPoliciesSummaryOfAssetsAndLiabilitiesMeasuredAtFairValueOnRecurringBasisDetails"></roleRef>
  <roleRef xlink:type="simple" xlink:href="pacb-20200630.xsd#DisclosureCashCashEquivalentsAndInvestmentsSummaryOfCashCashEquivalentsAndInvestmentsDetails" roleURI="http://www.pacificbiosciences.com/role/DisclosureCashCashEquivalentsAndInvestmentsSummaryOfCashCashEquivalentsAndInvestmentsDetails"></roleRef>
  <roleRef xlink:type="simple" xlink:href="pacb-20200630.xsd#DisclosureCashCashEquivalentsAndInvestmentsSummaryOfContractualMaturitiesOfCashEquivalentsAndAvailableForSaleInvestmentsDetails" roleURI="http://www.pacificbiosciences.com/role/DisclosureCashCashEquivalentsAndInvestmentsSummaryOfContractualMaturitiesOfCashEquivalentsAndAvailableForSaleInvestmentsDetails"></roleRef>
  <roleRef xlink:type="simple" xlink:href="pacb-20200630.xsd#DisclosureBalanceSheetComponentsComponentsOfInventoryDetails" roleURI="http://www.pacificbiosciences.com/role/DisclosureBalanceSheetComponentsComponentsOfInventoryDetails"></roleRef>
  <roleRef xlink:type="simple" xlink:href="pacb-20200630.xsd#DisclosureCommitmentsAndContingenciesScheduleOfAmountTimingAndUncertaintyOfCashFlowsFromOperatingLeasesDetails" roleURI="http://www.pacificbiosciences.com/role/DisclosureCommitmentsAndContingenciesScheduleOfAmountTimingAndUncertaintyOfCashFlowsFromOperatingLeasesDetails"></roleRef>
  <roleRef xlink:type="simple" xlink:href="pacb-20200630.xsd#DisclosureCommitmentsAndContingenciesScheduleOfAmountTimingAndUncertaintyOfCashFlowsFromOperatingLeasesDetailsAlternativeCalc" roleURI="http://www.pacificbiosciences.com/role/DisclosureCommitmentsAndContingenciesScheduleOfAmountTimingAndUncertaintyOfCashFlowsFromOperatingLeasesDetailsAlternativeCalc"></roleRef>
  <calculationLink xlink:role="http://www.pacificbiosciences.com/role/StatementCondensedConsolidatedBalanceSheets" xlink:type="extended" xlink:title="00100 - Statement - Condensed Consolidated Balance Sheets">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_Assets" xlink:label="us-gaap_Assets"></loc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AssetsCurrent" xlink:label="us-gaap_AssetsCurrent_637323161530693905"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_AssetsCurrent_637323161530693905" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CashAndCashEquivalentsAtCarryingValue" xlink:label="us-gaap_CashAndCashEquivalentsAtCarryingValue_637323161530713935"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent_637323161530693905" xlink:to="us-gaap_CashAndCashEquivalentsAtCarryingValue_637323161530713935" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShortTermInvestments" xlink:label="us-gaap_ShortTermInvestments_637323161530713935"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent_637323161530693905" xlink:to="us-gaap_ShortTermInvestments_637323161530713935" order="2" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccountsReceivableNetCurrent" xlink:label="us-gaap_AccountsReceivableNetCurrent_637323161530713935"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent_637323161530693905" xlink:to="us-gaap_AccountsReceivableNetCurrent_637323161530713935" order="3" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_InventoryNet" xlink:label="us-gaap_InventoryNet_637323161530713935"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent_637323161530693905" xlink:to="us-gaap_InventoryNet_637323161530713935" order="4" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PrepaidExpenseAndOtherAssetsCurrent" xlink:label="us-gaap_PrepaidExpenseAndOtherAssetsCurrent_637323161530713935"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsCurrent_637323161530693905" xlink:to="us-gaap_PrepaidExpenseAndOtherAssetsCurrent_637323161530713935" order="5" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:label="us-gaap_PropertyPlantAndEquipmentNet_637323161530713935"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_PropertyPlantAndEquipmentNet_637323161530713935" order="2" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OperatingLeaseRightOfUseAsset" xlink:label="us-gaap_OperatingLeaseRightOfUseAsset_637323161530713935"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_OperatingLeaseRightOfUseAsset_637323161530713935" order="3" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RestrictedCashAndCashEquivalentsNoncurrent" xlink:label="us-gaap_RestrictedCashAndCashEquivalentsNoncurrent_637323161530713935"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_RestrictedCashAndCashEquivalentsNoncurrent_637323161530713935" order="4" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OtherAssetsNoncurrent" xlink:label="us-gaap_OtherAssetsNoncurrent_637323161530713935"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Assets" xlink:to="us-gaap_OtherAssetsNoncurrent_637323161530713935" order="5" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LiabilitiesAndStockholdersEquity" xlink:label="us-gaap_LiabilitiesAndStockholdersEquity"></loc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_Liabilities" xlink:label="us-gaap_Liabilities_637323161530823931"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesAndStockholdersEquity" xlink:to="us-gaap_Liabilities_637323161530823931" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LiabilitiesCurrent" xlink:label="us-gaap_LiabilitiesCurrent_637323161530823931"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities_637323161530823931" xlink:to="us-gaap_LiabilitiesCurrent_637323161530823931" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccountsPayableCurrent" xlink:label="us-gaap_AccountsPayableCurrent_637323161530823931"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent_637323161530823931" xlink:to="us-gaap_AccountsPayableCurrent_637323161530823931" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccruedLiabilitiesCurrent" xlink:label="us-gaap_AccruedLiabilitiesCurrent_637323161530823931"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent_637323161530823931" xlink:to="us-gaap_AccruedLiabilitiesCurrent_637323161530823931" order="2" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ContractWithCustomerLiabilityCurrent" xlink:label="us-gaap_ContractWithCustomerLiabilityCurrent_637323161530823931"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent_637323161530823931" xlink:to="us-gaap_ContractWithCustomerLiabilityCurrent_637323161530823931" order="3" use="optional" weight="1" priority="1"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OperatingLeaseLiabilityCurrent" xlink:label="us-gaap_OperatingLeaseLiabilityCurrent_637323161530823931"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent_637323161530823931" xlink:to="us-gaap_OperatingLeaseLiabilityCurrent_637323161530823931" order="4" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="pacb-20200630.xsd#pacb_DeferredGainFromReverseTerminationFee" xlink:label="pacb_DeferredGainFromReverseTerminationFee_637323161530823931"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent_637323161530823931" xlink:to="pacb_DeferredGainFromReverseTerminationFee_637323161530823931" order="5" use="optional" weight="1" priority="1"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OtherLiabilitiesCurrent" xlink:label="us-gaap_OtherLiabilitiesCurrent_637323161530823931"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent_637323161530823931" xlink:to="us-gaap_OtherLiabilitiesCurrent_637323161530823931" order="6" use="optional" weight="1" priority="3"></calculationArc>
    <loc xlink:type="locator" xlink:href="pacb-20200630.xsd#pacb_NotesPayableNetOfDiscountCurrent" xlink:label="pacb_NotesPayableNetOfDiscountCurrent_637323161530823931"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesCurrent_637323161530823931" xlink:to="pacb_NotesPayableNetOfDiscountCurrent_637323161530823931" order="7" use="optional" weight="1" priority="1"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ContractWithCustomerLiabilityNoncurrent" xlink:label="us-gaap_ContractWithCustomerLiabilityNoncurrent_637323161530823931"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities_637323161530823931" xlink:to="us-gaap_ContractWithCustomerLiabilityNoncurrent_637323161530823931" order="2" use="optional" weight="1" priority="1"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OperatingLeaseLiabilityNoncurrent" xlink:label="us-gaap_OperatingLeaseLiabilityNoncurrent_637323161530823931"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_Liabilities_637323161530823931" xlink:to="us-gaap_OperatingLeaseLiabilityNoncurrent_637323161530823931" order="3" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_StockholdersEquity" xlink:label="us-gaap_StockholdersEquity_637323161530823931"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesAndStockholdersEquity" xlink:to="us-gaap_StockholdersEquity_637323161530823931" order="2" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PreferredStockValue" xlink:label="us-gaap_PreferredStockValue_637323161530833929"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity_637323161530823931" xlink:to="us-gaap_PreferredStockValue_637323161530833929" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CommonStockValue" xlink:label="us-gaap_CommonStockValue_637323161530833929"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity_637323161530823931" xlink:to="us-gaap_CommonStockValue_637323161530833929" order="2" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AdditionalPaidInCapital" xlink:label="us-gaap_AdditionalPaidInCapital_637323161530833929"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity_637323161530823931" xlink:to="us-gaap_AdditionalPaidInCapital_637323161530833929" order="3" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax" xlink:label="us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax_637323161530833929"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity_637323161530823931" xlink:to="us-gaap_AccumulatedOtherComprehensiveIncomeLossNetOfTax_637323161530833929" order="4" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit_637323161530833929"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_StockholdersEquity_637323161530823931" xlink:to="us-gaap_RetainedEarningsAccumulatedDeficit_637323161530833929" order="5" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CommitmentsAndContingencies" xlink:label="us-gaap_CommitmentsAndContingencies_637323161530833929"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesAndStockholdersEquity" xlink:to="us-gaap_CommitmentsAndContingencies_637323161530833929" order="3" use="optional" weight="1" priority="2"></calculationArc></calculationLink>
  <calculationLink xlink:role="http://www.pacificbiosciences.com/role/StatementCondensedConsolidatedStatementsOfOperationsAndComprehensiveLoss" xlink:type="extended" xlink:title="00200 - Statement - Condensed Consolidated Statements of Operations and Comprehensive Loss">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ComprehensiveIncomeNetOfTax" xlink:label="us-gaap_ComprehensiveIncomeNetOfTax"></loc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss_637323161530843918"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_ComprehensiveIncomeNetOfTax" xlink:to="us-gaap_NetIncomeLoss_637323161530843918" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OperatingIncomeLoss" xlink:label="us-gaap_OperatingIncomeLoss_637323161530843918"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss_637323161530843918" xlink:to="us-gaap_OperatingIncomeLoss_637323161530843918" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_GrossProfit" xlink:label="us-gaap_GrossProfit_637323161530843918"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingIncomeLoss_637323161530843918" xlink:to="us-gaap_GrossProfit_637323161530843918" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RevenueFromContractWithCustomerIncludingAssessedTax" xlink:label="us-gaap_RevenueFromContractWithCustomerIncludingAssessedTax_637323161530843918"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_GrossProfit_637323161530843918" xlink:to="us-gaap_RevenueFromContractWithCustomerIncludingAssessedTax_637323161530843918" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CostOfGoodsAndServicesSold" xlink:label="us-gaap_CostOfGoodsAndServicesSold_637323161530843918"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_GrossProfit_637323161530843918" xlink:to="us-gaap_CostOfGoodsAndServicesSold_637323161530843918" order="2" use="optional" weight="-1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OperatingExpenses" xlink:label="us-gaap_OperatingExpenses_637323161530843918"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingIncomeLoss_637323161530843918" xlink:to="us-gaap_OperatingExpenses_637323161530843918" order="2" use="optional" weight="-1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ResearchAndDevelopmentExpense" xlink:label="us-gaap_ResearchAndDevelopmentExpense_637323161530843918"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingExpenses_637323161530843918" xlink:to="us-gaap_ResearchAndDevelopmentExpense_637323161530843918" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_SellingGeneralAndAdministrativeExpense" xlink:label="us-gaap_SellingGeneralAndAdministrativeExpense_637323161530843918"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingExpenses_637323161530843918" xlink:to="us-gaap_SellingGeneralAndAdministrativeExpense_637323161530843918" order="2" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_GainLossOnContractTermination" xlink:label="us-gaap_GainLossOnContractTermination_637323161530843918"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss_637323161530843918" xlink:to="us-gaap_GainLossOnContractTermination_637323161530843918" order="2" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_InterestExpense" xlink:label="us-gaap_InterestExpense_637323161530843918"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss_637323161530843918" xlink:to="us-gaap_InterestExpense_637323161530843918" order="3" use="optional" weight="-1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OtherNonoperatingIncomeExpense" xlink:label="us-gaap_OtherNonoperatingIncomeExpense_637323161530843918"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetIncomeLoss_637323161530843918" xlink:to="us-gaap_OtherNonoperatingIncomeExpense_637323161530843918" order="4" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OtherComprehensiveIncomeAvailableforsaleSecuritiesAdjustmentNetOfTaxPortionAttributableToParent" xlink:label="us-gaap_OtherComprehensiveIncomeAvailableforsaleSecuritiesAdjustmentNetOfTaxPortionAttributableToParent_637323161530843918"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_ComprehensiveIncomeNetOfTax" xlink:to="us-gaap_OtherComprehensiveIncomeAvailableforsaleSecuritiesAdjustmentNetOfTaxPortionAttributableToParent_637323161530843918" order="2" use="optional" weight="1" priority="2"></calculationArc></calculationLink>
  <calculationLink xlink:role="http://www.pacificbiosciences.com/role/StatementCondensedConsolidatedStatementsOfCashFlows" xlink:type="extended" xlink:title="00500 - Statement - Condensed Consolidated Statements of Cash Flows">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseExcludingExchangeRateEffect" xlink:label="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseExcludingExchangeRateEffect"></loc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseExcludingExchangeRateEffect" xlink:to="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss_637323161530853938"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="us-gaap_NetIncomeLoss_637323161530853938" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_GainLossOnContractTermination" xlink:label="us-gaap_GainLossOnContractTermination_637323161530853938"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="us-gaap_GainLossOnContractTermination_637323161530853938" order="2" use="optional" weight="-1" priority="3"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_Depreciation" xlink:label="us-gaap_Depreciation_637323161530853938"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="us-gaap_Depreciation_637323161530853938" order="3" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="pacb-20200630.xsd#pacb_OperatingLeaseRightOfUseAssetAmortization" xlink:label="pacb_OperatingLeaseRightOfUseAssetAmortization_637323161530853938"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="pacb_OperatingLeaseRightOfUseAssetAmortization_637323161530853938" order="4" use="optional" weight="1" priority="1"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AmortizationOfFinancingCostsAndDiscounts" xlink:label="us-gaap_AmortizationOfFinancingCostsAndDiscounts_637323161530853938"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="us-gaap_AmortizationOfFinancingCostsAndDiscounts_637323161530853938" order="5" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_GainLossOnSaleOfDerivatives" xlink:label="us-gaap_GainLossOnSaleOfDerivatives_637323161530853938"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="us-gaap_GainLossOnSaleOfDerivatives_637323161530853938" order="6" use="optional" weight="-1" priority="3"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ShareBasedCompensation" xlink:label="us-gaap_ShareBasedCompensation_637323161530853938"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="us-gaap_ShareBasedCompensation_637323161530853938" order="7" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_InvestmentIncomeNetAmortizationOfDiscountAndPremium" xlink:label="us-gaap_InvestmentIncomeNetAmortizationOfDiscountAndPremium_637323161530853938"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="us-gaap_InvestmentIncomeNetAmortizationOfDiscountAndPremium_637323161530853938" order="8" use="optional" weight="-1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncreaseDecreaseInAccountsReceivable" xlink:label="us-gaap_IncreaseDecreaseInAccountsReceivable_637323161530853938"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="us-gaap_IncreaseDecreaseInAccountsReceivable_637323161530853938" order="9" use="optional" weight="-1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncreaseDecreaseInInventories" xlink:label="us-gaap_IncreaseDecreaseInInventories_637323161530853938"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="us-gaap_IncreaseDecreaseInInventories_637323161530853938" order="10" use="optional" weight="-1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets" xlink:label="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets_637323161530863933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="us-gaap_IncreaseDecreaseInPrepaidDeferredExpenseAndOtherAssets_637323161530863933" order="11" use="optional" weight="-1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncreaseDecreaseInAccruedLiabilities" xlink:label="us-gaap_IncreaseDecreaseInAccruedLiabilities_637323161530863933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="us-gaap_IncreaseDecreaseInAccruedLiabilities_637323161530863933" order="12" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncreaseDecreaseInAccountsPayable" xlink:label="us-gaap_IncreaseDecreaseInAccountsPayable_637323161530863933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="us-gaap_IncreaseDecreaseInAccountsPayable_637323161530863933" order="13" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncreaseDecreaseInOtherCurrentLiabilities" xlink:label="us-gaap_IncreaseDecreaseInOtherCurrentLiabilities_637323161530863933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="us-gaap_IncreaseDecreaseInOtherCurrentLiabilities_637323161530863933" order="14" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_IncreaseDecreaseInContractWithCustomerAsset" xlink:label="us-gaap_IncreaseDecreaseInContractWithCustomerAsset_637323161530863933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="us-gaap_IncreaseDecreaseInContractWithCustomerAsset_637323161530863933" order="15" use="optional" weight="-1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OperatingLeasePayments" xlink:label="us-gaap_OperatingLeasePayments_637323161530863933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="us-gaap_OperatingLeasePayments_637323161530863933" order="16" use="optional" weight="-1" priority="3"></calculationArc>
    <loc xlink:type="locator" xlink:href="pacb-20200630.xsd#pacb_IncreaseDecreaseInDeferredGainFromReverseTerminationFee" xlink:label="pacb_IncreaseDecreaseInDeferredGainFromReverseTerminationFee_637323161530863933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInOperatingActivities_637323161530843918" xlink:to="pacb_IncreaseDecreaseInDeferredGainFromReverseTerminationFee_637323161530863933" order="17" use="optional" weight="1" priority="1"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetCashProvidedByUsedInInvestingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInInvestingActivities_637323161530863933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseExcludingExchangeRateEffect" xlink:to="us-gaap_NetCashProvidedByUsedInInvestingActivities_637323161530863933" order="2" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PaymentsToAcquirePropertyPlantAndEquipment" xlink:label="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment_637323161530873968"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities_637323161530863933" xlink:to="us-gaap_PaymentsToAcquirePropertyPlantAndEquipment_637323161530873968" order="1" use="optional" weight="-1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_PaymentsToAcquireInvestments" xlink:label="us-gaap_PaymentsToAcquireInvestments_637323161530873968"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities_637323161530863933" xlink:to="us-gaap_PaymentsToAcquireInvestments_637323161530873968" order="2" use="optional" weight="-1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities" xlink:label="us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities_637323161530873968"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInInvestingActivities_637323161530863933" xlink:to="us-gaap_ProceedsFromMaturitiesPrepaymentsAndCallsOfAvailableForSaleSecurities_637323161530873968" order="3" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_NetCashProvidedByUsedInFinancingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInFinancingActivities_637323161530873968"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_CashCashEquivalentsRestrictedCashAndRestrictedCashEquivalentsPeriodIncreaseDecreaseExcludingExchangeRateEffect" xlink:to="us-gaap_NetCashProvidedByUsedInFinancingActivities_637323161530873968" order="3" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="pacb-20200630.xsd#pacb_ProceedsFromContractTermination" xlink:label="pacb_ProceedsFromContractTermination_637323161530873968"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities_637323161530873968" xlink:to="pacb_ProceedsFromContractTermination_637323161530873968" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_RepaymentsOfNotesPayable" xlink:label="us-gaap_RepaymentsOfNotesPayable_637323161530883943"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities_637323161530873968" xlink:to="us-gaap_RepaymentsOfNotesPayable_637323161530883943" order="2" use="optional" weight="-1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_ProceedsFromIssuanceOfCommonStock" xlink:label="us-gaap_ProceedsFromIssuanceOfCommonStock_637323161530883943"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_NetCashProvidedByUsedInFinancingActivities_637323161530873968" xlink:to="us-gaap_ProceedsFromIssuanceOfCommonStock_637323161530883943" order="3" use="optional" weight="1" priority="2"></calculationArc></calculationLink>
  <calculationLink xlink:role="http://www.pacificbiosciences.com/role/DisclosureSummaryOfSignificantAccountingPoliciesSummaryOfAssetsAndLiabilitiesMeasuredAtFairValueOnRecurringBasisDetails" xlink:type="extended" xlink:title="40302 - Disclosure - Summary of Significant Accounting Policies (Summary of Assets and Liabilities Measured at Fair Value on a Recurring Basis) (Details)">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AssetsFairValueDisclosure" xlink:label="us-gaap_AssetsFairValueDisclosure"></loc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure" xlink:label="us-gaap_CashAndCashEquivalentsFairValueDisclosure_637323161530883943"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsFairValueDisclosure" xlink:to="us-gaap_CashAndCashEquivalentsFairValueDisclosure_637323161530883943" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_InvestmentsFairValueDisclosure" xlink:label="us-gaap_InvestmentsFairValueDisclosure_637323161530893933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsFairValueDisclosure" xlink:to="us-gaap_InvestmentsFairValueDisclosure_637323161530893933" order="2" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="pacb-20200630.xsd#pacb_LongTermRestrictedCashFairValueDisclosure" xlink:label="pacb_LongTermRestrictedCashFairValueDisclosure_637323161530893933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AssetsFairValueDisclosure" xlink:to="pacb_LongTermRestrictedCashFairValueDisclosure_637323161530893933" order="3" use="optional" weight="1" priority="1"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LiabilitiesFairValueDisclosure" xlink:label="us-gaap_LiabilitiesFairValueDisclosure"></loc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_DerivativeLiabilities" xlink:label="us-gaap_DerivativeLiabilities_637323161530893933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesFairValueDisclosure" xlink:to="us-gaap_DerivativeLiabilities_637323161530893933" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="pacb-20200630.xsd#pacb_ContractTermination" xlink:label="pacb_ContractTermination_637323161530893933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LiabilitiesFairValueDisclosure" xlink:to="pacb_ContractTermination_637323161530893933" order="2" use="optional" weight="1" priority="1"></calculationArc></calculationLink>
  <calculationLink xlink:role="http://www.pacificbiosciences.com/role/DisclosureCashCashEquivalentsAndInvestmentsSummaryOfCashCashEquivalentsAndInvestmentsDetails" xlink:type="extended" xlink:title="40401 - Disclosure - Cash, Cash Equivalents and Investments (Summary of Cash, Cash Equivalents and Investments) (Details)">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AvailableForSaleSecuritiesAmortizedCost" xlink:label="us-gaap_AvailableForSaleSecuritiesAmortizedCost"></loc>
    <loc xlink:type="locator" xlink:href="pacb-20200630.xsd#pacb_AvailableForSaleSecuritiesGrossUnrealizedGainAccumulatedInInvestments" xlink:label="pacb_AvailableForSaleSecuritiesGrossUnrealizedGainAccumulatedInInvestments_637323161530893933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AvailableForSaleSecuritiesAmortizedCost" xlink:to="pacb_AvailableForSaleSecuritiesGrossUnrealizedGainAccumulatedInInvestments_637323161530893933" order="1" use="optional" weight="-1" priority="3"></calculationArc>
    <loc xlink:type="locator" xlink:href="pacb-20200630.xsd#pacb_AvailableForSaleSecuritiesGrossUnrealizedLossAccumulatedInInvestments" xlink:label="pacb_AvailableForSaleSecuritiesGrossUnrealizedLossAccumulatedInInvestments_637323161530893933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AvailableForSaleSecuritiesAmortizedCost" xlink:to="pacb_AvailableForSaleSecuritiesGrossUnrealizedLossAccumulatedInInvestments_637323161530893933" order="2" use="optional" weight="1" priority="3"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AvailableForSaleSecurities" xlink:label="us-gaap_AvailableForSaleSecurities_637323161530893933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AvailableForSaleSecuritiesAmortizedCost" xlink:to="us-gaap_AvailableForSaleSecurities_637323161530893933" order="3" use="optional" weight="1" priority="2"></calculationArc></calculationLink>
  <calculationLink xlink:role="http://www.pacificbiosciences.com/role/DisclosureCashCashEquivalentsAndInvestmentsSummaryOfContractualMaturitiesOfCashEquivalentsAndAvailableForSaleInvestmentsDetails" xlink:type="extended" xlink:title="40402 - Disclosure - Cash, Cash Equivalents and Investments (Summary of Contractual Maturities of Cash Equivalents and Available-for-Sale Investments) (Details)">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecurities"></loc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent_637323161530893933"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AvailableForSaleSecuritiesDebtSecurities" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesCurrent_637323161530893933" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecuritiesNoncurrent" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesNoncurrent_637323161530903951"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_AvailableForSaleSecuritiesDebtSecurities" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecuritiesNoncurrent_637323161530903951" order="2" use="optional" weight="1" priority="2"></calculationArc></calculationLink>
  <calculationLink xlink:role="http://www.pacificbiosciences.com/role/DisclosureBalanceSheetComponentsComponentsOfInventoryDetails" xlink:type="extended" xlink:title="40502 - Disclosure - Balance Sheet Components (Components of Inventory) (Details)">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_InventoryNet" xlink:label="us-gaap_InventoryNet_635888865099742422"></loc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_InventoryRawMaterialsNetOfReserves" xlink:label="us-gaap_InventoryRawMaterialsNetOfReserves_637323161530903951"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_InventoryNet_635888865099742422" xlink:to="us-gaap_InventoryRawMaterialsNetOfReserves_637323161530903951" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_InventoryWorkInProcessNetOfReserves" xlink:label="us-gaap_InventoryWorkInProcessNetOfReserves_637323161530903951"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_InventoryNet_635888865099742422" xlink:to="us-gaap_InventoryWorkInProcessNetOfReserves_637323161530903951" order="2" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_InventoryFinishedGoodsNetOfReserves" xlink:label="us-gaap_InventoryFinishedGoodsNetOfReserves_637323161530903951"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_InventoryNet_635888865099742422" xlink:to="us-gaap_InventoryFinishedGoodsNetOfReserves_637323161530903951" order="3" use="optional" weight="1" priority="2"></calculationArc></calculationLink>
  <calculationLink xlink:role="http://www.pacificbiosciences.com/role/DisclosureCommitmentsAndContingenciesScheduleOfAmountTimingAndUncertaintyOfCashFlowsFromOperatingLeasesDetails" xlink:type="extended" xlink:title="40602 - Disclosure - Commitments and Contingencies (Schedule of Amount, Timing and Uncertainty of Cash Flows from Operating Leases) (Details)">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue"></loc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueAfterYearFive" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueAfterYearFive_637323161530903951"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueAfterYearFive_637323161530903951" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour_637323161530903951"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearFour_637323161530903951" order="2" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree_637323161530903951"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearThree_637323161530903951" order="3" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo_637323161530903951"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueYearTwo_637323161530903951" order="4" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsRemainderOfFiscalYear" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsRemainderOfFiscalYear_637323161530903951"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsRemainderOfFiscalYear_637323161530903951" order="5" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonths" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonths_637323161530903951"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDueNextTwelveMonths_637323161530903951" order="6" use="optional" weight="1" priority="2"></calculationArc></calculationLink>
  <calculationLink xlink:role="http://www.pacificbiosciences.com/role/DisclosureCommitmentsAndContingenciesScheduleOfAmountTimingAndUncertaintyOfCashFlowsFromOperatingLeasesDetailsAlternativeCalc" xlink:type="extended" xlink:title="40602 - Disclosure - Commitments and Contingencies (Schedule of Amount, Timing and Uncertainty of Cash Flows from Operating Leases) (Details) (Alternative Calc)">
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue"></loc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_LesseeOperatingLeaseLiabilityUndiscountedExcessAmount" xlink:label="us-gaap_LesseeOperatingLeaseLiabilityUndiscountedExcessAmount_637323161530903951"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_LesseeOperatingLeaseLiabilityUndiscountedExcessAmount_637323161530903951" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OperatingLeaseLiability" xlink:label="us-gaap_OperatingLeaseLiability_637323161530903951"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_LesseeOperatingLeaseLiabilityPaymentsDue" xlink:to="us-gaap_OperatingLeaseLiability_637323161530903951" order="2" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OperatingLeaseLiabilityCurrent" xlink:label="us-gaap_OperatingLeaseLiabilityCurrent_637323161530903951"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingLeaseLiability_637323161530903951" xlink:to="us-gaap_OperatingLeaseLiabilityCurrent_637323161530903951" order="1" use="optional" weight="1" priority="2"></calculationArc>
    <loc xlink:type="locator" xlink:href="http://xbrl.fasb.org/us-gaap/2020/elts/us-gaap-2020-01-31.xsd#us-gaap_OperatingLeaseLiabilityNoncurrent" xlink:label="us-gaap_OperatingLeaseLiabilityNoncurrent_637323161530903951"></loc>
    <calculationArc xlink:type="arc" xlink:arcrole="http://www.xbrl.org/2003/arcrole/summation-item" xlink:from="us-gaap_OperatingLeaseLiability_637323161530903951" xlink:to="us-gaap_OperatingLeaseLiabilityNoncurrent_637323161530903951" order="2" use="optional" weight="1" priority="2"></calculationArc></calculationLink></linkbase>
