We report herein a case of distal bile duct carcinoma showing intestinal differentiation diagnosed 3 years after endoscopic sphincterotomy for choledocholithiasis. The diagnostic problem in this case was that the granular mucosa, which is a typical finding of superficial mucosal extension of bile duct carcinoma in general, was interpreted as hyperplasia accompanying metaplasia in cholangioscopic biopsy. Discrimination of superficial mucosal cancer extension from hyperplastic mucosa with metaplastic changes was impossible using cholangioscopic examination. In our case, reflux and stasis of the duodenal and pancreatic juice into the biliary tract might have occurred because of abnormal function of the papilla of Vater following endoscopic sphincterotomy. It might be suggested that endoscopic sphincterotomy contributed to the metaplastic changes in the bile duct mucosa in our case.