We reviewed our experience of Roux-en-Y hepaticojejunostomy (RYHJ) and hepaticoduodenostomy (HD) performed for the surgical repair of choledochal cyst (CC), with special emphasis on postoperative complications related to the type of biliary reconstruction performed. Eighty-six patients underwent primary cyst excision for CC from 1986 to 2002 at our institution. Forty-six cases with concurrent intrahepatic bile duct dilatation (IHBD) were excluded because HD was not used for biliary reconstruction if IHBD was present. Thus, 28 cases had RYHJ, and 12 had HD. Differences between the RYHJ and HD groups with respect to type of CC, age at cyst excision, and length of follow-up were not statistically significant. However, the incidences of postoperative complications related to biliary reconstruction, such as endoscopy-proven bilious gastritis due to duodenogastric bile reflux [4/12 (33.3%) of the HD group], and adhesive bowel obstruction/cholangitis [2/28 (7.1%) of the RYHJ group] were significantly different (p<.05). Our experience suggests that HD is not ideal for biliary reconstruction in CC because of a high incidence (33.3%) of complications due to duodenogastric bile reflux. Currently, RYHJ is our exclusive technique of choice for biliary reconstruction during the surgical repair of CC.