PurposeTo report our experience with a modified biliary-enteric anastomosis procedure for the surgical treatment of congenital choledochal cysts.MethodsBetween January 2009 and December 2013, 91 children (19 boys, 72 girls; ages, 6–145 months) with congenital choledochal cysts were treated with our modified surgical procedure in our hospital. Of these patients, 69 had type I cysts, and 22 had type IV B cysts. The main parameters analyzed mainly included the operative time, duration of bowel recovery, resumption of diet, postoperative hospital stay, liver-function tests, postoperative complications, and prognosis.ResultsThe average operation duration was 129.34 ± 23.50 min. The time until first flatus and resumption of oral diet were 26.51 ± 4.13 h and 5.47 ± 0.77 day, respectively. The mean postoperative hospital stay was 11.84 ± 2.58 day. Postoperative complications occurred in six patients: intestinal obstruction (1 patient), postoperative bleeding (1 patient), postoperative pancreatitis (1 patient), and bile leakage (3 patients). During a follow-up of 2–7 years, four cases of occasional abdominal pain were found. Contrast agent reflux was detected on upper gastrointestinal imaging in three children. All children had good nutrition.ConclusionThe modified biliary-enteric anastomosis is a safe, simple, and reliable technique. However, longer follow-up and a larger sample size are necessary to prove its efficacy in the treatment of congenital choledochal cysts.