Choledochal cysts have been associated with complications such as cholangitis, pancreatitis, and malignancy of the biliary tract. Recently, the incidence of choledochal cyst in neonate and young infant is increasing due to advances in diagnostic imaging. The aim of this study is to investigate the rationale of excision of choledochal cyst during the neonatal period. The clinical outcome and correlation between age at surgery and the degree of liver fibrosis were reviewed retrospectively. A total of 198 patients with choledochal cyst who were managed surgically between January 1985 and December 2000 at the Department of Surgery, Seoul National University Children's Hospital were included in this study. The overall outcome and the outcome of patients who were managed surgically during the neonatal period were compared. Correlation between age and the degree of liver fibrosis was evaluated by chi-square test and Pearson exact test. The mean age of the patients was 2 years 7 months (ranged from 5 days to 15 years). Mean postoperative follow-up period was 7 years 1 month (7 months to 20 years). The results are as follows. Twelve patients (6%) had postoperative complications, cholangitis (7), bleeding (4) and ileus (1). Eleven patients operated during the neonatal period had no postoperative complications. The positive correlation between age group and degree of liver fibrosis was statistically significant (chi-square: p=0.0165, Pearson exact test: p=0.019). The results support the rationale that excision of choledochal cyst can be performed safely without increasing morbidity in neonates.