We investigate the incidence, treatment, and implications of intrahepatic bile duct (IHBD) dilatation debris in 42 patients with choledochal cyst treated over a recent 8-year period. Mean age at cyst excision was 6.9 years, and mean follow-up period was 5.4 years. Intraoperative endoscopy (IOE) was performed at the time of cyst excision using a pediatric cystoscope, which identified IHBD debris in 11/42 (26.2%), and massive debris in 4/42 (9.5%). In all cases, IHBD debris was successfully washed out with normal saline through the cystoscope. There was no postoperative IHBD stone formation or cholangitis except for one case of cholangitis in a patient undergoing chemotherapy for acute myelocytic leukemia. Debris left in the IHBD during cyst excision is probably one of the primary causes of postoperative IHBD stone formation and can be prevented by washing during IOE.