Background Congenital cystic dilatation of the extra- and intrahepatic bile ducts is a rare condition with several potential complications, especially a high risk of malignant degeneration, which may develop from an anomalous arrangement of the pancreatico-biliary ductal junction. Patients Twenty-two patients with cystic dilatation of the biliary tree, subdivided according to the Todani classification, were observed and treated during a 17-year period. The intrahepatic ducts were involved in 15 patients. Results Surgical treatment involved either total excision of extrahepatic cysts, hepatic resection in cases of segmental intrahepatic disease or, in the presence of diffuse intrahepatic disease, a wide biliary-digestive anastomosis performed onto the biliary confluence, with the intent of reducing the risk of neoplastic degeneration. One patient with extensive and symptomatic liver involvement complicated by biliary cirrhosis has already undergone liver transplantation, and another two patients who are currently asymptomatic may require this procedure in future. Neoplastic degeneration was found in three patients (one each of Todani type I, type IVa and type V), or 14% of the series. The postoperative course was complicated by cholangitis in only two patients, who were treated successfully with antibiotics. Except for one patient with a type I cyst complicated by carcinoma, who died 14 months post-operatively, all patients are alive and well at a mean follow-up of eight years (range 8 months to 17 years). Discussion The ideal surgical procedures to cure the disease and prevent malignant degeneration are: (a) complete excision of the extrahepatic biliary cysts; (b) hepatic resection in cases of segmental intrahepatic involvement; (c) wide bilio-digestive anastomosis in cases of multiple intrahepatic involvement, or liver transplantation when this is complicated by secondary biliary cirrhosis.