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Enteritis cystica profunda is a very rare disease in which a mucin-filled cystic space is surrounded partially with nonneoplastic columnar epithelium in the submucosa of the small intestine. Most of the cases are accompanied by intestinal diseases, and the disease usually occurs in the jejunum and the ileum and there has been no report of a case that occurred in the ampulla of Vater. A 58-year-old healthy female patient without any particular symptom visited the hospital to get additional examination for a mass found on the ampulla of Vater by accident. In esophagogastroduodenoscopy, a cystic mass showing a positive pillow sign was found on the ampulla of Vater. Endoscopic retrogradecholangiopancreatography was conducted as choledochocele was suspected, but no abnormality was found in the biliary system. In endoscopic ultrasonography, multiseptated cystic structures were detected in the submucosal layer of the duodenum. The lesion was resected completely through endoscopic snare polypectomy and the case was histologically diagnosed as enteritis cystica profunda.