It is often difficult to establish the diagnosis of intestinal tuberculosis because of close similarities with other conditions, in particular, Crohn's disease. In the present study, we used the polymerase chain reaction (PCR) assay on endoscopic biopsy specimens obtained from a patient with chronic diarrhea. Positive hybridization was obtained with the Mycobacterium tuberculosis probe and the patient was treated with anti-tuberculous drugs with complete resolution of the endoscopic abnormalities. This study demonstrates that polymerase chain reaction assay can be used on endoscopic biopsy specimens to diagnose intestinal tuberculosis.