A 47-year-old man presented with an abnormality of the duodenum detected on a health check endoscopy. Further endoscopy revealed swelling of the papilla of Vater with a whitish exudate and surrounding small nodules, which biopsy revealed to be non-caseating granulomas. Colonoscopy showed typical tubercular lesions in the colon on the right side, so we speculated that the lesions of the papilla of Vater were tubercular. After the administration of anti-tubercular drugs, both the duodenal lesion and the colonic lesions improved. Therefore, the papilla of Vater lesion was diagnosed as tubercular, although such cases are extremely rare.