The purpose of this study was to validate the usefulness of transesophageal echocardiography (TEE) in the assessment of cardiovascular shunts in patients with pulmonary hypertension (PH) of unexplained cause. Twenty-four adult patients, 16 women, 8 men; 15 to 70 years of age, with PH of unexplained cause were studied. All were examined by transthoracic echocardiography (TTE) and TEE. TTE showed the ventricular septal defect in two patients, muscular type in one and perimembranous type in the other. TEE showed the atrial septal defect in eight patients (secundum type in six and primum type in the remaining) and the patient ductus arteriosus in six patients, which were not seen by TTE. The ventricular septal defect shown by TTE was also found by TEE. Patients with a ventricular septal defect were also associated with a patient ductus arteriosus. Among 14 patients with cardiovascular lesions, nine patients displayed a pattern of bidirectional shunt, four a pure left-to-right shunt, and the remaining one a pure right-to-left shunt. All of the cardiovascular defects could be confirmed by passage of the catheter across the defect at cardiac catheterization. In light of PH, transthoracic identification of cardiovascular shunts is difficult because of the low velocity across the defect. In this study, we found that TEE was superior to TTE in detecting and localizing cardiovascular malformations in patient with PH.