PURPOSE: The level of bile amylase in a choledochal cyst varies although the theory of pancreaticobiliary reflux through an anomalous pancreaticobiliary duct union (APBDU) is widely accepted as a cause of choledochal cysts. The aim of this study was to evaluate the clinical characteristics of choledochal cysts according to the level of bile amylase in the cyst. METHODS: During the last 17 years, 59 pediatric choledochal cyst patients were surgically treated at the division of Pediatric Surgery, Keimyung University Dongsan Medical Center. Of those patients, 42 in whom the level of bile amylase in the cyst was measured at operation were included in this study. The age, duration clinical findings, anatomical types and the types of Anomalous pancreaticobiliary duct union (APBDU) were analyzed after subdividing the patients into 3 groups according to the bile amylase activity in their cysts: group N, <100 U/L, group 1, 100 U/L~0, 000 U/L, and group 2, >10, 000 U/L. RESULTS: The mean ages in groups 1, 2, and N were 5.0+/-4.7 years, 6.2+/-3.7, and 1.7+/-2.4 years, respectively with group 2 being the eldest (P=0.005). Eighty percent of group 2 had long histories of symptom duration (longer than 1 month), with recurrent abdominal pain and/or hospitalization and the diagnosis of pancreatitis, which was also higher than the 37 and 42% in groups N and 1, respectively (P=0.038). Jaundice and an abdominal mass were the predominant symptoms in the group N, whereas abdominal pain, jaundice and vomiting were predominant in the groups 1 and 2. According to the Todani's classification, the incidence of type IV was higher than type I in all groups, with the ratio of 1: 2. According to the Komi's classification of the APBDU, the incidence of Komi I and II in groups 1 and 2 were similar, with the ratio of 1: 2. CONCLUSION: The level of bile amylase in choledochal cysts was significantly higher with advancing age, especially in patients having a long history of recurrent attacks of abdominal pain and pancreatitis. However, there were no significant difference among the 3 groups with respect to the anatomical cyst type and type of APBDU. Therefore, further studies are necessary to determine the correlation between the cyst type and the pathogenesis and pathophysiology, and the see if choledochal cysts have a close relationship with APBDU and pancreatitis.