The prevalence and morphologic characteristics of atrial septal aneurysms identified by transesophageal echocardiography in 410 consecutive patients are described. Two groups of patients were compared: Group I consisted of 133 patients referred for evaluation of the potential source of an embolus and Group II consisted of 277 patients referred for other reasons. An atrial septal aneurysm was diagnosed by transesophageal echocardiography in 32 (8%) of the 410 patients. Surface echocardiography identified only 12 of these aneurysms. Atrial septal aneurysm was significantly more common in patients with stroke (20 [15%] of 133 vs. 12 [4%] of 277) (p less than 0.05); right to left shunting at the atrial level was demonstrated in 70% of patients in Group I and 75% of patients in Group II by saline contrast echocardiography. Four patients in Group I had an atrial septal defect with additional left to right flow. There was no difference between the two groups in aneurysm base width, total excursion or left atrial or right atrial excursion. However, Group I patients had a thinner atrial septal aneurysm than did Group II patients. It is concluded that an atrial septal aneurysm occurs commonly in patients with unexplained stroke, is more frequently detected by transesophageal echocardiography than by surface echocardiography and is usually associated with right to left atrial shunting. Treatment (anticoagulant therapy vs. surgery) of atrial septal aneurysm identified in stroke patients can be determined only by long-term follow-up studies.