BACKGROUND/AIMS Few reports have appeared on the development of acute pancreatitis in children with choledochal cysts and no information on optimal timing of surgery is available. We assessed patient outcomes relative to timing of surgery and serum amylase and lipase concentrations. METHODOLOGY We reviewed 29 patients < or = 15 years old with acute pancreatitis, as evidenced by abdominal pain, increased serum amylase and lipase concentrations (>200 IU/L for each), and radiological examination, who underwent surgery for congenital choledochal cysts between 2000 and 2010. RESULTS Patients were divided into three groups according to timing of surgery. At the time of operation, serum amylase and lipase concentrations were significantly higher in patients who underwent early surgery. Change in hemoglobin concentration, length of operation, time of diet commencement after surgery, and hospitalization days, were similar in the three groups. Many patients for whom surgery was delayed underwent endoscopic retrograde cholangiopancreatography (ERCP). When patients were divided into three groups according to serum amylase and lipase concentrations at the time of operation, no statistically significant differences in surgical parameters or outcomes were evident. CONCLUSIONS Early cyst excision following development of acute pancreatitis in patients with choledochal cysts reduces patient symptoms and decreases the need for ERCP.