Biopsies are necessary for the management of duodenal tumors. However, the most suitable targets for biopsy are not known. An 82-year-old woman who regularly visited our hospital for rheumatoid arthritis underwent abdominal ultrasonography. This screening revealed a dilated pancreatic duct. Magnetic resonance cholangiopancreatography was performed, and dilatation of the pancreatic duct was confirmed. The patient underwent duodenoscopy to investigate the possibility of obstruction of the papilla of Vater. The examination revealed an elevated lesion around the papilla of Vater. Endoscopic ultrasonography and a 20-MHz mini-probe were used to investigate the depth of the invasion. The common bile and pancreatic ducts were intact. The mucosal and submucosal borders were indistinct; however, the border between the submucosa and muscularis propria was clear, suggesting that the muscularis propria was intact. Magnifying endoscopy was used to examine the surface of the elevated lesion, which revealed a depressed lesion. A biopsy specimen of the depressed lesion was taken, and the tumor was diagnosed as an adenocarcinoma. Another biopsy specimen from a non-depressed lesion was diagnosed as an adenoma. The patient was diagnosed with duodenal adenocarcinoma, and was recommended surgery. She declined surgery and was followed up for 34 months. Because it is possible for depressed lesions of duodenal tumors to be adenocarcinomas, biopsy specimens should be obtained from depressed lesions of duodenal tumors.