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Aim: Intestinal tuberculosis (ITb) and Crohn's disease (CD) mimic each other often leading to misdiagnosis. We evaluated the difference between ITb and CD using the extent of apoptosis in peripheral blood lymphocytes., Methods: CD4 + cells as a percentage of the lymphocytes and viable, dead, total apoptotic, early apoptotic, and late apoptotic CD4 + cells were assessed in the peripheral blood by flow cytometry in healthy controls and patients with confirmed active ITb and CD prior to initiating therapy. Early apoptotic and total apoptotic cells were further expressed as a proportion of the percentage of CD4 + cells., Results: The percentages of CD4 + cells (6.5 [3.0, 8.7] vs. 13.40 [10.15, 13.40]; p < 0.001), total apoptotic cells (0.13 [0.0, 0.22] vs. 0.08 [0.0, 0.21]; p = 0.045), early apoptotic (1.24 [0.55, 2.54] vs. 0.71 [0.40, 1.30]; p = 0.037), and the proportion of the latter two parameters (17.18 [5.61, 57.33] vs. 4.84 [2.71, 9.83]; p-value 0.039) and (17.18 [7.4, 67.50] vs. 5.51 [3.10, 11.03]; p-value 0.036) were significantly different between patients with ITb and CD. The best sensitivity, specificity, and positive and negative predictive values for the diagnosis of ITb were seen with the CD4 + cell percentage (82.6%, 82.4%, 86.4%, 77.8%, respectively) and the proportion of early apoptotic cells (73.9%, 70.6%, 77.3%, 66.7%, respectively)., Conclusion: CD4 + cells as a percentage of peripheral blood lymphocytes and the proportion of early apoptotic CD4 + cells show promise to diagnostic differentiation between ITb and CD.