We report a case of pulmonary embolism complicated by paradoxical cerebral embolism in a patient with atrial septal aneurysm and patent foramen ovale. The patient was a 65-year-old obese woman, admitted because of sudden development of right-sided hemiplegia and dysarthria. In the few days before hospitalization she noted painful edema of the right leg and suffered from increasing dyspnea. Echo-Doppler examination of the venous bed confirmed the clinical suspicion of deep vein thrombosis. A pulmonary scan showed multiple perfusion defects in both lungs. On cerebral computerized tomography there were two non-haemorrhagic infarct zones. Contrast transesophageal echocardiography revealed a type II atrial septal aneurysm with right-to-left shunting through a patent foramen ovale. The patient was treated by warfarin, followed by implantation of a caval filter, with a good outcome. Paradoxical embolism may be more common than currently thought. In cases of pulmonary embolism, a careful check for clinical symptoms indicative of a possible paradoxical embolism should be performed and, consequently, a search for possible atrial septal aneurysm or patent foramen ovale.