Objective To summarize the experience of open heart operation on neonates with critical and complex congenital heart diseases and evaluate the methods of perioperative management. Methods From May 2001 to January 2003, 12 patients of neonates with congenital heart diseases underwent emergency operation. Their operating ages ranged from 6 to 30 days, the body weights were 2.8 to 4.5 kg. Their diagnoses included D-transposition of the great arteries in 4 cases, ventricular septal defect with atrial septal defect in 5 cases, complete atrioventricular septal defect, obstructed supracardiac total anomalous pulmonary venous drainage and cardiac rhabdomyomas in 1 case respectively. 12 cases were operated under moderate or deep hypothermic cardiopulmonary bypass. Results All cases were observed in ICU for 2-11 days and discharged 7-19 days after operation. The postoperative complications included low cardiac output, mediastinal infection, respiratory distress syndrome, systemic capillary leak syndrome and acute renal failure. All cases were cured and the follow-up (from 6 months to 2 years) showed satisfactory outcome. Conclusion A particular cardiopulmonary bypass and proper perioperative management is very important to ensure the successful outcome. Peritoneal dialysis is an effective and safe method for treating acute renal failure after cardiac operation in neonates.