Duodenogastric reflux (DGR) was assessed in patients surgically treated for choledochal cyst, with emphasis on two different biliary reconstruction methods: Roux-en-Y hepaticojejunostomy (HJ) and hepaticoduodenostomy (HD). Gastric bile monitoring with the Bilitec device revealed excessive DGR in patients in the HD group. Endoscopic findings demonstrated mild to moderate gastric mucosal erosion in patients after HD. In contrast, neither DGR nor gastritis was found in patients after HJ. This preliminary study suggests that HJ, rather than HD, should be recommended as a method of biliary reconstruction for pediatric patients with choledochal cyst. Careful observation of DGR should be continued in patients who have undergone HD.