A patent foramen ovale (PFO) is found by transesophageal echocardiography in one half of patients with cryptogenic stroke (CS). Coagulation abnormalities may promote paradoxical emboli in these patients. Seventeen patients were identified with PFO and CS. Thirty-one percent of patients had hematologic risk factors for venous thrombosis. These included abnormal activated protein C resistance and increased anticardiolipin antibodies. Patients with coagulation abnormalities and a PFO were three times as likely to be treated with warfarin compared to aspirin (P<0.05). Prothrombotic states are common in patients with PFO and CS and identifying these conditions may impact the choice of antithrombotic therapy.