Abstract: Objective To determine the values of short-term anti-tuberculosis treatment in the differential diagnosis of Crohn’s disease (CD) and intestinal tuberculosis (ITB). Methods A review of cases (from January 2009 to October 2013) with a 2-3 month therapeutic trial of anti-tuberculosis was performed. The clinical manifestation and endoscopic findings of the patients, and the accuracy, sensitivity and specificity of the short term anti-tuberculosis trial for differential diagnosis of ITB and CD were analysed. Results Sixty-four cases entered into study, with 33 diagnosed with ITB and 31 with CD. In the ITB patients, 31 had significant improvement in their clinical and endoscopic manifestations, with decreased erythrocyte sedimentation rate (ESR) and C-reactive portein (CRP) (\P\P<0.05). On the contrary, only three CD patients showed improvement in their disease activity （CDAI）. The accuracy of short-term anti-tuberculosis treatment in the differential diagnosis was 92.19%, with a sensitivity and specificity of 93.94% and 90.32%, respectively. There was no significant difference in CDAI scores in the CD patients prior to and after 2-3 months trial of anti-tuberculosis treatment. Conclusion Short term trial of anti-tuberculosis treatment is valuable and feasible in the differential diagnosis of ITB and CD.