Paradoxical embolism through a patent foramen ovale (PFO) is a recognized cause of stroke, but its prognosis is not well known. The aim of our study is to evaluate differences in risk factors, recurrent stroke subtypes and effects of various preventive therapies between PFO associated stroke patients with and without deep vein thrombosis (DVT). A total of 63 patients who had an embolic stroke with a PFO within 3 months from stroke onset were enrolled. Venous ultrasonography, which was performed in all the patients, revealed DVT in 26 patients (41%). Venous thrombosis was confined to the isolated calf veins in 24 of 26 cases (92%). For prevention of stroke recurrence, warfarin was administrated in 32 patients, antiplatelet therapy was given in 21 patients, and combination of warfarin and antiplatelet therapy was chosen in 10 patients. Three patients with DVT and three other patients without DVT had recurrent ischemic events during a mean follow-up period of 14.6 months. In all the 3 patients without DVT, complicated aortic arch lesions were also observed, and 2 of them had lacunar infarcts. In all the three patients with DVT recurrent embolic stroke or TIA occurred in spite of anticoagulant therapy. Their INR values at the time of recurrence were all below 1.7, and 2 of them were associated with atrial septal aneurysm (ASA). Association with PFO, ASA, and DVT may be a substantial risk factor for recurrent stroke. Higher INR value in anticoagulation may be recommended for such patients to prevent stroke recurrence.