The aetiology of stroke in young patients is usually difficult to establish. Despite extensive investigations, the cause of stroke remains unknown in a large percentage of these patients. We report a case of stroke in a young patient in whom the only associated aetiological factor was a lone atrial septal aneurysm. We discuss the investigational tools in the diagnosis of atrial septal aneurysms and study the aetiopathogenesis of strokes and the risk of recurrent strokes associated with their presence. We also review the evidence for the presently available therapies for prevention of further strokes in such patients.