Background: Tuberculosis is a major global health concern, particularly in India, where it accounts for 10-15% of total TB cases. Extrapulmonary tuberculosis (EPTB) accounts for 20% and are often undetected due to its diverse clinical presentation and lack of diagnostic means. Mycobacterium tuberculosis complex organisms (MTBC) cause TB primarily in the lungs but can affect other organs, causing EPTB. Diagnosis of EPTB is challenging due to low numbers of MTB bacilli and difficulty in obtaining clinical specimens. Early detection of tuberculosis and multidrug resistance is crucial to reduce complications and mortality. Conventional microscopy and culture are essential for early diagnosis, but they are expensive, time-consuming, and require a long time to detect bacilli. The GeneXpert MTB/RIF assay, an automated real-time PCR system, has high sensitivity and specificity for the diagnosis of MTB as compared to ZN smear microscopy that can detect M. tuberculosis and rifampicin resistance with less turnaround time (two hours),which has proven itself as an effective tool in initiation of early treatment of suspected extra-pulmonary tuberculosis.In this study we compare the CBNAAT positive results with ZN staining to understand the sensitivity percentage. Aim: This study, at Microbiology department of Chirayu Medical College & Hospital, India, aimed to understand CBNAAT positivity prevalence in extra-pulmonary tuberculosis cases, and correlate it with smear microscopy from February 2023 to July 2023. Data was collected, analysed, and a correlation was established between CBNAAT and ZN microscopy. Method: This study involved 565 samples of suspected extra-pulmonary tuberculosis cases. The samples received from IPD and OPD were divided into two parts;one for ZN staining and the other for GeneXpert. The GeneXpert MTB/RIF assay runs within 2 hours and results are interpreted as the presence of MTB with RIF resistance detection. For ZN staining, fluid specimens are concentrated by centrifugation and the sediment was used directly. Smears are prepared and stained with Ziehl-Neelsen staining method according to NTEP guidelines. The statistical data collected were analysed for sensitivity and specificity for GeneXpert assay and ZN staining. The project analysis focused on positive cases obtained from GeneXpert MTB/RIF results. Results: In this study of six-month period, 565 patient samples found 105 (18.6%) cases of CBNAAT as positive reports, while 460 (81.4%) as negative reports. The majority of positive cases were from the IPD, with a gender distribution of 41 males and 64 females. The age distribution was 0-20 years, with 21 patients aged 0-20 years and 50 patients aged 31-60 years. The study found that only 2.9% of Ziehl-Neelsen staining cases showed positivity, indicating that the CBNAAT was able to detect Mycobacterium tuberculosis (MTB) at high and medium detection levels. The CBNAAT was able to achieve very low detection levels, with 97% of RIF susceptibility and only 5% resistance. The CBNAAT is an important development in rapid molecular TB diagnostics, endorsed by the World Health Organization (WHO) as an effective molecular technique for early diagnosis, treatment, and control of TB. It detects DNA specific for Mycobacterium tuberculosis by polymerase chain reaction. Conclusion: The GeneXpert MTB/RIF assay is a reliable method for detecting EPTB with high sensitivity and specificity, making it suitable for resource-constrained settings. Its fast turnaround time and minimal infrastructure requirement make it ideal for areas with high risk of MDR-TB or HIV-associated TB. CBNAAT, a more sensitive technique, has a higher positivity rate than AFB smear, making it a better choice for rapid disease diagnosis.