Background and Aim: The differentiation between Crohn's disease (CD) and tuberculosis (TB) of the intestine can be difficult in areas where both diseases occur. The present study examined histological criteria that would enable the diagnosis in mucosal biopsies. Methods: Colonoscopic biopsies from 33 patients with TB and 31 patients with CD were examined for several specific histological features and their distribution. Results: The salient distinguishing features of TB were granulomas larger than 400 μm in maximum dimension, more than four sites of granulomatous inflammation per site, caseation, a band of epithelioid histiocytes in ulcer bases and location of granulomas in the caecum. The salient features of CD were granulomas not showing any of the above features, focally enhanced colitis, pericryptal granulomatous inflammation, and the presence of architectural alteration/activity/chronic inflammation/deep ulceration at sites that did not show granulomatous response in the same or adjacent segments. Although granulomas in CD were distributed throughout the colon, they were more frequent in the rectosigmoid than in TB. All biopsies from endoscopically abnormal sites did not show distinguishing features of TB or CD, emphasizing the need for multiple biopsies. There was an accrual in the number of diagnoses made with increasing numbers of biopsies from rectum to ileum. Conclusions: Histology of mucosal biopsies can aid in the differentiation of TB from CD, but multiple biopsies from different colonic segments are important for complete evaluation. © 2005 Blackwell Publishing Asia Pty Ltd.