We compared surgical outcomes of the single-stage and two-stage modified Fontan procedures to clarify clinical superiority. Of 28 children undergoing a modified Fontan procedure from October 1995 to October 2005, 15 had a 1-stage and 13 had a 2-stage operation. In the 2-stage group, pulmonary artery growth was evaluated before and after the first stage. Operative mortality was 26.6% in the 1-stage group and 0% in the 2-stage group. The benefits of a previous bidirectional Glenn shunt were decreased cyanosis and volume overload, but there was no significant difference in pulmonary artery growth reflected in pulmonary artery indices before and after the bidirectional Glenn procedure. Older children underwent a 2-stage modified Fontan procedure and had better outcomes in terms of lower mortality, improved oxygen saturation, decreased volume load, and less deterioration of atrioventricular valve regurgitation.