The　deformation　of　capsules　(i.e.,　cells,　bacterial)　in　microscale　flows　plays　an　important　role　in　biofluid　flows　such　as　blood　flow　in　capillaries　and　cell　manipulation　in　microfluidics.　In　previous　studies　on　capsule　deformation　in　microscale　flows,　the　inertia　effect　was　often　assumed　to　be　negligible　and　thus　omitted.　However,　this　assumption　may　not　reflect　real　situations,　as　indicated　by　recent　studies　of　inertial　microfluidics.　As　such,　we　aimed　to　study　the　inertia　effect　on　capsule　deformation　in　microscale　flows　and　to　determine　under　which　conditions　this　effect　may　be　omitted.　Using　a　collocated　grid　projection　scheme,　we　developed　a　finite　difference-front　tracking　method,　and　investigated　the　deformation　of　viscoelastic　capsules　in　microscale　flows　for　Reynolds　number　(Re)　ranging　from　0.01　to　10　as　seen　in　vitro　and　in　vivo.　The　results　showed　that　the　transient　and　steady-state　deformation　of　capsules　was　significantly　affected　by　inertia,　and　the　flow　structure　varied　considerably　when　Re　was　varied　from　0.1　to　10.　No　significant　changes　were　found　for　Re　ranging　from　0.01　to　0.1,　and　hence　the　inertia　effect　on　capsule　deformation　in　the　microscale　flows　can　be　omitted　when　Re　is　less　than　0.1.　These　findings　improve　the　current　understanding　of　the　mechanism　underlying　cell　movement　in　capillaries　and　can　be　applied　to　optimize　the　conditions　for　cell　manipulation　and　separation　in　microfluidic　devices.