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Choledochocele (type 3 choleduct cyst) is rarely seen in children. Here we report the case of a 5-year-old female who complained of abdominal pain for 2 years. A choledochocele with a diameter of 31 mm localized on the second part of the duodenum, in the periampullary region, was detected. Upper gastrointestinal endoscopy revealed a mass starting from the second part of the duodenum and constricting the duodenal lumen. A 2-cm-long incision was made at the apex of the cyst using a needle tip sphincterectome and three 5- to 6-mm stones were extracted. There were no postoperative complications.