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A patient with an acute ischemic stroke had an interatrial septal aneurysm shown by transesophageal echocardiography. Interatrial shunting, compatible with a patent foramen ovale, was observed on a follow-up study after a second stroke. This was seen in association with a right atrial thrombus. This case illustrates that an interatrial septal aneurysm serves as a marker for potential interatrial shunting, which can lead to paradoxical cerebral embolism.