A three-year-old girl with complex cardiac anomalies and right isomerism successfully underwent a modified Fontan procedure and reconstruction of the nonconfluent pulmonary artery using autologous tissues. These cardiac anomalies included single right ventricle, atresia of the pulmonary trunk with nonconfluent pulmonary artery, atrial septal defect, common atrioventricular valve, bilateral PDAs, and bilateral SVCs. Preoperative cardiac catheterization showed elevated pulmonary artery pressure (mean pressure of 24 mmHg) and a small orifice of common pulmonary vein chamber. Pulmonary arteriographies showed balanced development of the branches. Indication for Fontan procedure was finally determined by measurement of the pulmonary artery and vein pressures and pulmonary vascular resistance before the cardiopulmonary bypass in the operation. Nonconfluent pulmonary artery was reconstructed by direct anastomosis of the right and left branches in the posterior aspect and enlarged with autologous pericardium patch. Intracardiac anomalies were repaired by enlargement of common pulmonary vein orifice (from 5 mm to 15 mm in diameter) and right atrial oblique partition. Furthermore, Fontan circulation was established by pulmonary artery angioplasty, direct anastomosis of left SVC to left pulmonary artery and direct anastomosis of right atrial appendage to pulmonary artery. Postoperative clinical course was uneventful, and cardiac catheterization showed mean right atrial pressure of 14 mmHg, cardiac index of 3.5 l/min/m2, and no pressure gradient at the site of reconstruction of the pulmonary artery.