A 70-year old woman, with a history of recent thromboembolic stroke, was admitted to our hospital because of sudden dyspnea due to pulmonary thromboembolism. Transthoracic echocardiography revealed a tubular thrombus entrapped in a patent foramen ovale. Transesophageal echocardiography confirmed this finding and also revealed an atrial septal aneurysm. Because her cerebral status contraindicated surgical intervention, medical therapy with heparin and warfarin was started. Follow-up transthoracic echocardiography, performed 3 weeks after the initiation of therapy, revealed complete resolution of the thrombus. Medical therapy can be an alternative to surgical therapy in high-risk patients who have entrapped thrombi.