The therapies for treating tumors of the papilla of Vater remain controversial because accurate preoperative diagnosis is difficult. Treatments include endoscopic resection, pancreaticoduodenectomy and total papillectomy. We report the case of a 69-year-old man who underwent total papillectomy for a borderline malignant tumor of the papilla of Vater. In our institution, the decision to perform a total papillectomy for borderline malignant adenoma is based on whether it is intestinal type or pancreaticobiliary type. Carcinoma of the papilla of Vater is classified into two types: an intestinal type and a pancreaticobiliary type and the prognosis of the intestinal type is much better than that of the pancreaticobiliary type. We suggest that total papillectomy can be performed for an intestinal, borderline malignant tumor.