Background: Extrapulmonary tuberculosis (EPTB) often possesses a diagnostic dilemma in comparison to pulmonary tuberculosis which can be easily diagnosed by simple microscopy. Paucibacillary nature of specimens giving negative smear for acid fast bacilli, lack of granulomas on histopathology and failure to culture Mycobacterium tuberculosis do not exclude the diagnosis of EPTB. To overcome these limitations novel diagnostic methods of nucleic acid amplification like Polymerase Chain Reaction have been reported with good sensitivity and rapidity for diagnosis of EPTB. Polymerase Chain Reaction PCR could have a significant advantage over the conventional methods for early diagnosis of clinically suspected cases of EPTB. Objectives: 1) The present study was conducted to evaluate the role of PCR using MPB64 species specific primer in early diagnosis of extrapulmonary tuberculosis. 2) To compare the results of PCR v/s microscopy and culture. Material and Methods: A total of 100 clinical specimens comprising pleural fluid, cerebrospinal fluid, ascitic fluid, fine needle aspiration biopsy, pus and biopsy from clinically suspected EPTB cases were included in the present study. These specimens were processed by conventional diagnostic methods i.e Microscopy by Ziehl Neelsen (ZN) stain and culture on Lowenstein Jensen (LJ) medium. The PCR was performed by using species specific MPB64 primer. Results: In the present study tuberculous pleural effusion (39%) followed by tubercular meningitis (31%) was found to be the commonest clinical presentation of EPTB. The overall positivity of PCR was 53% in patients with EPTB. Microscopy and culture could detect only 12% of these. On histopathological examination 100% positivity by PCR was seen in tissue samples suggestive of tuberculosis. Of the 77 EPTB patients who responded to antituberculosis treatment (ATT), 53 patients were PCR positive. Comparing the results of PCR visa `a vis conventional technique using response to the treatment as a gold standard the sensitivity and specificity of PCR was found to be 68.8% and 100% respectively. Conclusion: This study shows that PCR can serve as a useful complement when used along with conventional diagnostic methods in rapid diagnosis of EPTB.