Background and Objectives: Tuberculosis continues to have the highest number of TB cases in the world with over 2 million active TB cases every year. Extrapulmonary TB (EPTB) constitutes about 15 to 20% of all cases of TB. The conventional diagnostic methods are either slow or less sensitive in diagnosing EPTB. So there is a need for rapid and accurate diagnostic tests like molecular techniques such as RT-PCR. These tests would facilitate early diagnosis of potentially infectious patients and prompt institution of anti tubercular therapy. Aim & Objective: The present study intends to evaluate the diagnostic efficacy of RT-PCR, conventional AFB microscopy by ZN and Auramine stain, and culture by LJM and MB7H9 in the diagnosis of different forms of extrapulmonary tuberculosis taking Culture as gold standard. Methods: Clinically diagnosed patients of EPTB were subjected to RT-PCR (commercial kits). Out of these, 25 RT-PCR positive samples and 25 PCR negative samples were evaluated by microscopy and culture. A total of 24 DNA samples from PCR-positive cases tested using commercial kits, were subjected to an in-house RT-PCR test (IS6110 - 123 bp). Results: In the present study, the sensitivity, specificity, positive predictive value and negative predictive value of microscopy were found to be 37.5%, 94.44%, 81.8% and 69.38% respectively against gold standard culture. Sensitivity and specificity of RT-PCR was found to be 70.83%, 63.88%. Positive predictive value of RT-PCR was found to be 56.66% and negative predictive value was 76.66% against gold standard culture. Conclusion: EPTB is an important cause of morbidity and mortality. Laboratory diagnosis has many problems. Molecular techniques are rapid, sensitive and specific. However, all the available diagnostic methods should be utilized as RT-PCR is not 100% sensitive. The results need to be carefully correlated with clinical findings, to diagnose this disease.