A 60-year-old woman who had undergone cholecystectomy, choledocholithotomy and choledochoduodenostomy 21 years previously for cholecystolithiasis and choledocholithiasis, presented with nausea and vomiting. With a preoperative diagnosis of recurrent common bile duct stones, the extrahepatic bile duct was excised and choledochojejunostomy was performed. Histologic examination of the resected specimen disclosed chronic cholangitis, papillary epithelial hyperplasia, and mild dysplasia. Choledochoduodenostomy predisposes to reflux of duodenal contents, resulting in chronic mechanical and chemical irritation likely to induce histopathologic alterations in the bile duct mucosa. Since bile duct dysplasia induced by chronic inflammation may be a precursor of cancer, indication for choledochoduodenostomy should be specific and limited, and careful long-term follow-up is mandatory.