A 22-year-old man visited our hospital (National Cancer Center Hospital East) complaining of fatigue and anorexia. A laboratory investigation demonstrated a biochemical 'picture' of obstructive jaundice. An abdominal CT showed a low density mass in the retropancreatic area with multiple enlarged periportal lymph nodes. Upper gastrointestinal endoscopy revealed active ulceration on the dorsal wall of the descending part of the duodenum, and histopathology of the biopsy specimen revealed an ulcer with reactive inflammatory cell infiltration; no tumor cells were detected. The possibility of neoplasm had been ruled out by the use of CT and angiography. The jaundice recovered spontaneously and the abdominal mass gradually decreased in size. Endoscopic retrograde pancreatography showed no evidence of pancreatic disease; however, endoscopic retrograde cholangiography showed a choledocho-duodenal fistula. This patient showed hypersensitivity against the tuberculin skin test and Mycobacterium tuberculosis was successfully detected in gastric juice by using a polymerase chain reaction method and culture. Biopsy samples obtained from the duodenal ulcer at the second upper gastrointestinal endoscopy showed chronic inflammation with an epithelioid granuloma, suggesting tuberculosis. We thus diagnosed this case as a duodenal tuberculosis with a choledocho-duodenal fistula. To the best of our knowledge, there has been no report available of duodenal tuberculosis being the cause of a choledocho-duodenal fistula.