We report three consecutive cases of patients who had refractory hypoxemia and paradoxical embolism during the course of pulmonary embolism. Transesophageal echocardiography showed an atrial septal aneurysm and a patent foramen ovale in all patients. The latter was detected by an early and massive passage of contrast from the right to the left atrium. We suggest that the presence of an atrial septal aneurysm plus a patent foramen ovale greatly enhances both magnitude of shunting and the risk of systemic embolism. The presence of an atrial septal aneurysm plus a patent foramen ovale should be considered and checked using transesophageal echocardiography in every patient with significant pulmonary embolism.