Doppler echocardiography was used to evaluate blood flow in the pulmonary artery in 14 patients 2 to 42 months (mean (SD) 17 (12) months) after a modified Fontan operation incorporating a direct atriopulmonary anastomosis. Preoperatively six patients had tricuspid atresia, six had a double inlet left ventricle, and two had pulmonary atresia with an intact ventricular septum. The postoperative rhythm was sinus in 11 patients, junctional in one, ventricular pacing in one, and atrioventricular sequential pacing in one. In one patient the Doppler trace was unsatisfactory for analysis. In all patients forward flow in the pulmonary artery had biphasic peaks related to both atrial and ventricular contraction. The mean (SD) peak flow velocity that was synchronous with atrial contraction was 80 (30) cm/s and that synchronous with ventricular contraction was 74 (23) cm/s. The atrial contribution to total pulmonary artery flow, assessed by velocity-time integrals, varied between 22% and 73% (mean (SD) 45 (14)%). In patients with tricuspid atresia the mean (SD) peak flow velocity with atrial contraction was 90 (27) cm/s and that with ventricular contraction was mean (SD) 68 (24) cm/s. In patients with double inlet left ventricle the mean (SD) peak flow velocity was 67 (36) cm/s with atrial contraction and 80 (25) cm/s with ventricular contraction. The atrial contribution to total pulmonary blood flow in patients with tricuspid atresia was significantly higher (53 (11)%) than in those with double inlet left ventricle (37 (14)%). Pulmonary artery flow after modified Fontan operation was biphasic and was related to both atrial and ventricular contraction. The atrial contribution to pulmonary blood flow is greater in patients with tricuspid atresia than in those with a double inlet left ventricle. The mechanism of the second peak related to ventricular contraction is unknown.