Patients with ischemic stroke are sometimes found to have an underlying inherited (deficiency of protein C, protein S, antithrombin III, activated protein C resistance, prothrombin gene mutation, hyperhomocysteinemia) or acquired thrombophilia (lupus anticoagulant and anticardiolipin antibodies, hyperhomocysteinemia). Patient selection for thrombophilia screening is, therefore, a frequent question in managing patients with ischemic stroke. In this review we discuss patient selection and timing for laboratory tests for thrombophilia screening in stroke patients based on a literature review and we calculated overall costs per year in Germany for testing patients older than 18 years with an ischemic stroke of undetermined cause. As there is a lack of studies comparing anticoagulation with antiplatelet therapy in patients with diagnosed thrombophilia, laboratory screening for thrombophilia even in a selected group of patients with cryptogenic ischemic stroke remains of questionable value at present. An exception appears to be testing for lupus anticoagulant and anticardiolipin antibodies in younger patients with suspected antiphospholipid syndrome (two positive test results necessary), because anticoagulation seems to be superior to aspirin in patients with antiphospholipid syndrome.