Intrahepatic calculi complicate choledochal cysts in 7-8% of patients. Although congenital stenoses and dilatation of the intrahepatic bile ducts are considered responsible for calculi formation, intrahepatic calculi are usually formed after cyst excision. In this study, bile specimens from patients with choledochal cysts were cultured for bacteria. Results were retrospectively analyzed among the following groups: the primary excision group, consisting of 97 patients undergoing cyst excision as a primary treatment (mean age 5.0 years), the internal drainage group, consisting of 13 patients who had previous cyst-enterostomy at cyst excision (mean age 20.2 years); and the hepatolithiasis group, consisting of 12 patients with postoperative hepatolithiasis (mean age 24.2 years). Bacteria were present in the bile of 10 patients (76.9%) in the internal drainage group and in all patients (100%) in the hepatolithiasis group, but present in only 17 patients (17.5%) in the primary excision group (p<0.01). Polymicrobial infection with Gram-negative enterobacteria such as Escherichia coli and Klebsiella species was predominant in the internal drainage and hepatolithiasis groups, while nonenteric bacteria were found in the primary excision group. Bile infection through bilioenterostomy may play an important role in intrahepatic calculus formation after excision of a choledochal cyst.