The aim of this study is to provide an overview of the aetiology, clinical presentation, diagnostics and surgical treatment options for choledochal cysts with an emphasis on today’s surgical procedure of choice. Congenital bile duct cysts are rare anomalies which affect extrahepatic and/or intrahepatic bile ducts. They are divided in five types according to Todani classification. The most common type of congenital bile duct cysts is type I: fusiform dilatation of extrahepatic bile ducts. First symptoms usually occur during the early childhood. Nowadays, we can diagnose choledochal cysts prenatally or postnatally by ultrasound. Endoscopic retrograde cholangiopancreatography is used for a more detailed view of the biliary system in children. Recently, this method has been more and more replaced by non-invasive MR (magnetic resonance) cholangiopancreatography. Surgical methods used in the past such as cystduodenostomy and Roux-en-Y cystjejunostomy were accompanied by many complications such as recurrent cholangitis and biliary carcinoma. The surgical procedure of choice is now a total cyst excision with an internal drainage. The most commonly used biliodigestive anastomosis is Roux-en-Y hepaticojejunostomy. The procedure was firstly described by Saito in 1966 and, according to studies, heals more than 97% of patients. With the development of laparoscopic surgery, more and more procedures in paediatrics are performed with minimally invasive approach. Despite numerous successful laparoscopic surgeries described in literature, open surgery is still the method of choice.