Objective To evaluate the clinical outcomes of total cavopulmonary connection (TCPC) and bidirectional Glenn shunt for treating complex congenital heart diseases with single functional ventricles. Methods From January 2002 to May 2004, twelve children, who had complex congenital heart diseases with single functional ventricles, underwent TCPC and bidirectional Glenn shunt. Among them, male was 3 and female was 9. Ages were from 4 to 13 years and body weights were from 14 to 34 kilograms. The diseases included mitral atresia 1 case, tricuspid atresia 3 cases, right ectopic heart with transposition of great arteries 3 cases, D-transposition of great arteries 3 cases, and single ventricle 2 cases. Results Eleven children survived and one child died in acute renal failure 19 hours after operation. The hospital mortality was 8.3%. Four children had chyle-thorax postoperatively, and eight children had uneventful recovery. In the follow-up period, one child died 12 months postoperatively for pulmomary arteriovenous fistula, and there were no complications like severe arrhythmia, thrombosis and cerebral problems. Conclusions TCPC and bidirectional Glenn shunt are safe and effective techniques for treating complex congenital heart diseases with single functional ventricles, and the clinical outcomes are satisfactory. The key points for the successful operation are big enough cava-pulmonary anastomosis as well as aggressive perioperative management.