Objective: To investigate the diagnosis and treatment of adult congenital bile duct cysts (BDC). Methods: The clinical data of 53 adult patients with congenital BDC admitted from January 1996 to May 2012 were retrospectively analyzed. Results: All patients underwent operation. Of the patients, total cyst excision with Roux-en-Y hepaticojejunostomy was performed in 39 cases with types Ia, Ib and Ic BDC as well as in 4 cases with type II BDC, while another 3 cases with type Ia BDC underwent partial cyst excision plus Roux-en-Y hepaticojejunostomy; one case with type IVa BDC underwent left lateral hepatic lobectomy, total cyst excision, hepatic ducts plasty and Roux-en-Y hepaticojejunostomy, and another case of type IVa BDC underwent total cyst excision plus Roux-en-Y hepaticojejunostomy; one case with type V BDC underwent left intrahepatic bile duct cyst excision. Of the two patients who showed malignant change, one case underwent resection of the malignant cysts and dissection of local metastatic lymph nodes, and another underwent cyst excision and left intrahepatic bile duct tumor resection. Forty-two of the 53 patients were followed-up for 6 months to 3 years. All patients with benign disease were in excellent condition after surgery. Of the two cancer patients, one case died of tumor recurrence and multi-system organ failure 26 months after peration, and the other case had tumor recurrence and liver metastasis after 26 months and then underwent re-operation that included left hemihepatectomy, S5 resection and Roux-en-Y hepaticojejunostomy, but finally died two months after re-operation due to the tumor progression and multi-system organ failure. Conclusion: For adult congenital BDC, the selection of surgical procedure may significantly influence the final results, and the different clinical types require different surgical methods.