Stroke in children is a rare condition and has a multifactorial etiology. The association between ischemic stroke in young adults and some minor cardiac abnormalities such as atrial septal aneurysm with or without interatrial shunting has recently been reported: however, the pathogenetic mechanism still remains unclear. Genetic and acquired prothrombotic disorders are also risk factors for cerebral ischemic events in children. We report a case of ischemic stroke in a 10-year-old female child who was heterozygous for the prothrombin G20210A variant and who presented with an atrial septal aneurysm associated with an interatrial shunt. We hypothesize that these risk factors play a synergic role but their relative importance and whether alone they can determine cerebral embolism remain to be determined.