AIM To evaluate the clinical outcomes of patients with prenatally diagnosed choledochal cysts compared with those diagnosed after birth and the optimal timing of definitive treatment. METHODS Retrospective review of all patients who underwent primary choledochal cyst excision and Roux-en-Y hepaticojejunostomy from 1996 to 2006 at a single institution. RESULTS A total of 45 patients were included. Ten (22.2%) of the patients had prior prenatal diagnosis. The mean age at operation for this group was 4.4 months and mean follow up was 55.9 months. There was no operative complication or late morbidity. For the post-natal diagnosis group, the mean age at operation was 5.7 years (P < 0.000) and mean follow up period was 69 months. The most common presentation in this group was abdominal pain (31.4%), followed by pancreatitis (28.6%) and symptoms of cholestasis (25.7%). Early post-operative morbidities occurred in two (5.7%) patients. On long-term follow up, two (5.7%) further patients in the post-natal group developed complications. CONCLUSION Prenatal diagnosis of choledochal cysts results in earlier definitive surgery. More adverse complications were seen in those who had surgery at an older age. We therefore recommend early excision of choledochal cysts.