Introduction: Overlap of clinical, endoscopic and radiographic features, coupled with a poor microbiological yield makes differentiating Crohn’s disease (CD) from intestinal tuberculosis (ITB) challenging. A potential histological differentiating mechanism is the use of immunohistochemical staining for the mesenchymal stem cell marker CD73, as a pilot study showed ITB but not CD granulomas stained positive for this marker. The aim of this study was to assess the value of CD73 in differentiating ITB from CD granulomas in a South African cohort.Methods: Patients with confirmed CD or ITB were identified from a pathology database. Tissue sections were reviewed by a pathologist to confirm the presence of granulomas. These were then stained with a mouse monoclonal anti-CD73 antibody. The slides were examined together by a pathologist and gastroenterologist in a blinded manner for anti-CD73 staining around granulomas.Results: Ninety six cases were available for analysis; 50 cases of ITB and 46 cases of CD. Thirty percent of CD granulomas (14/46) stained positive for CD73, whereas CD73 positivity was seen in 52% (26/50) of cases of ITB. This was statistically significant (OR 2.48, 95% CI 1.1–5.72, p = .03). The area under the curve (AUC) was 0.61. Sensitivity of CD73 in predicting ITB was 52% and specificity was 70%. Overall CD73 staining of granulomas correctly classified only 60% of cases.Conclusions: In our study we have shown that significantly more patients with ITB express CD73 in their granulomas than those with CD. However the relatively poor sensitivity, specificity and AUC make this test unlikely to be of value in our clinical practice.