Bile duct cysts represent congenital abnormalities associated with biliopancreatic maljunction that may undergo malignant degeneration. We report herein the case of a 72-year-old male patient with cholangitis. MR-cholangiography and abdominal CT revealed a mass at the biliary-pancreatic-duodenal crossroads, extrahepatic biliary dilation up to 38 mm, and pancreas divisum. Gastroscopy found an infiltrative bulbar mucosa with adenocarcinoma in biopsy samples, and extrinsic bulging of the second duodenal portion. Endoscopic ultrasound showed a choledochal cystic dilation with solid contents, and FNA findings were nonspecific. ERCP confirmed an adenomatous papilla at the lower portion of the extrinsic formation, and a large cystic, saccular dilation of extrahepatic bile ducts (Todani Ia). Fistulotomy was required for deep cannulation of the proximal biliary tract, and attention was drawn to extruding polypoid lesions originating in the biliary epithelium, identified in biopsies as adenoma with dysplasia. Finally, a diagnosis was made of advanced adenocarcinoma in choledochal cyst.