Abstract Background Choledochal cyst is usually diagnosed in childhood. Early treatment can prevent further complication. We report on our series of patients over the past 30 years. Methods A retrospective study was performed on all pediatric patients who presented with choledochal cyst from January 1978 to December 2008. The main outcome measures recorded were the clinical presentation, management, and long-term outcome of the patients. Results Eighty-three patients presented to us during the caption period with a mean age at diagnosis of 45 months (0 month to 16 years). Diagnoses were made antenatally in 15 patients. The most common symptoms were abdominal pain (n = 39) and jaundice (n = 35). Seventy-five patients had surgery, in which 72 patients had resection of the cyst and Roux-en-Y hepaticojejunostomy. Ten were performed by laparoscopic means. We categorized the cysts based on the Todani classification. There was no mortality. No malignant change was documented. For those 4 who had Caroli disease, 2 underwent liver transplantation and 2 had hepatectomy. Overall early complication rate was 5.3% (4/75). Conclusions Complete excision of cyst with Roux-en-Y hepaticojejunostomy is the treatment of choice, and the late result is good. Laparoscopic surgery is feasible. Long-term follow-up is necessary. There is no evidence to suggest that some type IV cysts are the result of disease progression from type I cysts.