Atrial septal aneurysm (ASA) is a localized saccular deformity, generally at the level of fossa ovalis, which protrudes to the right or left atrium, or both. A possible relationship between ASA and cerebral ischemic events have been suggested in retrospective and case-control studies. The purpose of this study was to determine the embolic potential of ASA by following-up patients with this abnormality. Of the 2319 consecutive patients undergoing transesophageal echocardiogaphy (TEE) for various indications, we identified 65 (2.8%) patients with ASA. Forty-four of these who were in sinus rhythm and were contactable were followed-up prospectively for 2.3 years. Their mean age was 43.8 years. During the follow-up of 101.6 patient-years, one patient had a transient ischemic attack (TIA), whereas none of the patients suffered a stroke or other systemic thromboembolism. The patient who had the TIA had primary pulmonary hypertension, enlargement of the right heart chambers and a bidirectional and very mobile ASA, and an intact interatrial septum. She had no history of a previous cerebrovascular accident. As a result, the yearly incidence of a cerebral ischemic event was about 1% in our hospital based cohort. We conclude that ASA found on TEE may be associated with TIA and embolic stroke, but the risk seems to be low.