BACKGROUND: Bile duct cysts (BDCs) are a rare benign entity, but can transform to biliary tract cancer at a significant percentage if untreated. The incidence in western countries is low, whereas higher numbers are reported in the Asian population. METHODS: PubMed and Medline database was systematically searched for correlative publications, with a focus on the period from 2000 to 2010. RESULTS: Although most cases of BDC are detected in childhood, mostly due to jaundice, about one out of four cases reaches adulthood without diagnosis. The most common forms of BDC are types I and IV, following Todani's classification. Symptoms vary within a wide range of unspecific signs, but detection with non-invasive or invasive imaging is steadily improving. The major threat is malignant transformation, which can appear also in non-dilated parts of the biliary tree and even after a long period of time. Therefore complete excision of the extrahepatic biliary system, removal of the gallbladder and biliary reconstruction have been widely accepted as the therapy of choice. CONCLUSIONS: Although rare, bile duct cysts show a high incidence of malignancy. Therefore early surgical intervention with subsequent life-long follow up is mandatory.