Atrial septal aneurysms (ASA) are frequent findings on transesophageal echocardiographies. Whether they are more frequent in patients with cerebral ischemia of unknown cause remains unclear. We investigated this question in 154 consecutive patients with an ischemic stroke or transient ischemic attack. The 16 patients with ASA were younger, less likely to have arterial hypertension and more likely to have a patent foramen ovale (PFO) or an unknown cause of stroke, but they did not differ for number and side of infarcts, other demographic data and vascular risk factors. Patients with ASA unassociated to PFO were also more likely to have an unknown cause of stroke. These findings lead to the hypothesis that ASA might be sources of cerebral emboli.