Because of the similarity of the clinical symptoms, endoscopic, and pathological features, the differential diagnosis between Crohn's disease (CD) and intestinal tuberculosis (ITB) remains difficult, especially in a high-incidence area of tuberculosis (TB). Here we reported three patients with positive Ziehl-Neelsen stain in endoscopic mucosal biopsy specimens. They had a poor response to anti-TB therapy but a good response to immunosuppresses, infliximab, or surgery, and were finally diagnosed as CD. It was not clear that they were CD concomitant with mycobacteria infection or CD induced by mycobacteria infection. Further studies including more clinical cases and related animal models are needed. Our cases highlight the importance of considering the presence of CD in patients with positive Ziehl-Neelsen stain, which were failure to respond to anti-TB treatment.