Diagnosing intestinal (Luminal) tuberculosis is challenging due to limited yield of diagnostic modalities like CT scan, colonoscopy with blind ileal biopsies. GeneXpert MTB/RIF (Xpert) assays for diagnosing tuberculosis have been performed in the body secretions with excellent results. Its yield in stool is tested in this study. The study aims to evaluate the yield of GeneXpert assay in stool of suspected cases of intestinal tuberculosis. Hundred patients with suspected intestinal tuberculosis underwent routine biochemical tests, radiological investigations, colonoscopy with caecal and blind ileal biopsies for histopathology. Fresh stool samples were collected, processed for DNA extraction, tested using 2:1 ratio of GeneXpert reagent to sample to give positive or negative results for Mycobacterium tuberculosis and Rifampicin resistance. Out of hundred participants, 52% were female. Mean age was 28.21 ± 12.13. CT scan and colonoscopy findings suggestive of TB were present in 47% and 43% participants respectively. GeneXpert in stool was positive in 20% cases. Considering mucosal biopsy with histopathology of intestinal specimens as diagnostic of abdominal Tuberculosis, sensitivity and specificity of GeneXpert was 39.1% and 85.7% respectively. Stool GeneXpert assay offers an alternative approach to detect intestinal tuberculosis rapidly with good diagnostic accuracy. Although it cannot replace the AFB culture and histopathology but contribute for early diagnosis and management. © 2019 The Author(s).