Background: For several decades smear microscopy and conventional culture techniques have been the mainstay of diagnostic testing for pulmonary tuberculosis. Culture is considered as the “gold standard” for final determination, but it is slow and may take up to 2 to 8 weeks. Although smear microscopy for acid-fast bacilli (AFB) is rapid and inexpensive, it has poor sensitivity and a poor positive predictive value (PPV). Thus, rapid identification, which is essential for earlier treatment initiation, improved patient outcomes, and more effective public health interventions, relies on nucleic acid amplification techniques Objective:The aim of this study was comparing the two techniques (i.e., Gene Xpert and ZN stain) for detection of MTB in in smear-positive and smear-negative pulmonary and non-pulmonary clinical specimens. Methodology:Total 700 patients of all age groups having either pulmonary or extra pulmonary tuberculosis were included in the study. All collected sputum samples will be processed by ZN staining technique and GeneXpert /CBNAAT technique. Comparisons of these techniques were done after sputum samples examined. Result: Out of 273 total patients report positive results for ZN stain showed 271 patients showed resistance for CBNAAT and 2 of them showed negative result. 427 patients were found negative for ZN stain, out of them only 2 patients were resistant to the CBNAAT and 425 were negative to CBNAAT. Conclusion: ZN staining and CBNAAT was found to be equally sensitive and not only in the detection of acid-fast bacilli but it could also detect rifampicin resistance.