Background: The extrapulmonary tuberculosis (EPTB) is challenging to diagnose due to its pauci-bacillary nature. According to recent research, WHO recommends cartridge based nucleic acid amplification test (CBNAAT) to be used as initial diagnostic test in suspected cases of extrapulmonary tuberculosis. Aim of the present study is to assess the role of CBNAAT in comparison with cytomorphological features upon fine needle aspiration cytology (FNAC) and Ziehl-Neelson (ZN) stain in clinically suspected cases of EPTB.Methods: Present pilot study is descriptive cross-sectional study of 439 cases of clinically suspected EPTB over a period of 12 months (January 2019 to December 2019). After procedure of fine needle aspirates, smears were stained with routine H&E, papanicolaou stain and ZN stain. In the same setting, aspirate was also sent for CBNAAT. Results were obtained after detailed study.Results: Out of 439 cases, presumptive tuberculosis was diagnosed in 192 cases showing either epithelioid cell granulomas or caseous necrosis or both upon morphology, while overall 94 cases were positive on ZN stain and 146 cases were CBNAAT positive with the sensitivity of 84.04% and specificity of 80.57%.Conclusions: FNAC is the cheapest and simplest method to diagnose extrapulmonary tuberculosis, however those smears where tuberculosis cannot be diagnosed on FNAC like suppurative lesions, reactive lymphadenitis and low cellularity, CBNAAT plays a key role for the correct diagnosis thereby significantly reducing the morbidity and mortality.

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