Objective To evaluate the therapeutic effects of endoscopic treatment on biliary tract complications after liver transplantation. Methods The clinical data of 55 patients with biliary tract complications after liver transplantation undergoing endoscopic treatment from January 2006 to June 2009 were analyzed retrospectively. Results Ninety-eight times of endoscopic treatment were performed in 55 patients. There were 11 cases of biliary fistula, 4 cases of bile duct stricture with biliary fistula, 21 cases of bile duct stricture, 12 cases of bile duct stricture with biliary sludge or stones, 3 cases of biliary sludge or stones, 2 cases of angular distortion of the bile duct and papilla duodeni stenosis in 2 cases. Different procedures including biliary tract dilation, endoscopic nasobiliary drainage, endoscopic sphincterotomy, stone extraction technique and biliary stent placement were performed in different biliary tract complications. The endoscopic treatments were successful in 46 cases (83.6%). The procedure related complications were found in 13 times (13.3%). Conclusion Endoscopy may serve as the primary modality for treating biliary tract complications after liver transplantation with safety and effectiveness.