We report a case of 35-yr-old woman with early cancer in congenital choledochal cyst. She had a five-year history of intermittent right upper abdominal pain and intermittent jaundice. In this period she had a few abdominal ultrasonographies, but the cholelithiasis had not been found. Now, she was admitted to our hospital because she felt right upper abdominal pain with slight jaundice and subfebrile temperature four weeks ago. Abdominal ultrasonography showed enormous dilatation of the common bile duct, which was suspected as choledochal cyst. Computed tomography and endoscopic retrograde cholangiopancreatography revealed cystic dilatation of extrahepatic bile duct. An anomalous pancreaticobiliary junction was not found. The patient with congenital choledochal cyst was operated on. The excision of choledochal cyst was done with hepaticojejunostomy Roux-en-Y. There were no lymph nodes metastases. On the central part of choledochal cysts mucosa, it was shown a white plain area of thickness 0.3 cm and 0.8 cm in diameter. Histologically it was well-differentiated tubular adenocarcinoma, which was limited to the mucosa and which did not penetrate to other parts of the bile duct wall. From our knowledge, only small number cases of early cholangiocarcinoma in choledochal cyst were until now reported. Nearly eight years after the operation the patient feels very well, and has optimal working ability (Karnofsky 100%).