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Objective: To determine diagnostic accuracy of GeneXpert Assay and compare it with smear microscopy for AFB in terms of sensitivity, specificity on bronchial washings/bronchoalveolar lavage samples in sputum smear negative suspected tuberculosis. Study Design: A prospective cross sectional analytical study. Place and Duration of Study: Pulmonology Department, Pak Emirates Military Hospital Rawalpindi, from Jul to Dec 2018. Materials and Methods: Patients older than 12 years with suspected sputum negative tuberculosis were included in the study. Bronchoscopy findings were noted, bronchoalveolar lavage fluid/bronchial washings were taken. Samples were sent for AFB smear; GeneXpert Assay and Cultures. Data was analyzed in SPSS version 23. Results: A total of 224 patients were included in the study. 151 (67.4%) were males and 73 (32.6%) females. Mean age was 48.25 ± SD 18.21. Flexible bronchoscopy was diagnostic for tuberculosis in overall 42.4% (95/224) cases. Smear microscopy for AFB was positive in 53 (23.7%) cases, GeneXpert in 82 (36.6%) cases, culture in 66 (29%) cases while 6 cases (2.7%) showed rifampicin resistance on GeneXpert RIF resistance assay. Sensitivity, specificity, PPV and NPV of smear microscopy were 69.6%, 95.5%, 86.7%, 88.3% respectively whereas for GeneXpert they were 86.36%, 84.1%, 69.5%. 93.66% respectively; when compared to culture considered as gold standard. GeneXpert assay activity had statistically significant (p-value<0.01) association with smear and culture positivity. Conclusion: GeneXpert assay had higher sensitivity than AFB smear microscopy and it is a rapid and effective tool on bronchial washings, reducing the time constraint associated with culture based diagnosis and determining Rifampin Resistance simultaneously.