India has the World’s largest burden of tuberculosis and approximately 15- 20% of these cases have extrapulmonary disease (EPTB). The diagnosis of tuberculosis from tissue specimens is usually made by histopathological examination (HPE). However, histopathology does not always give specific findings and needs more than one week for final reporting. In 2013, WHO endorsed Xpert MTB/RIF assay for the rapid diagnosis of EPTB. In the present study the efficacy of this assay to diagnose tuberculosis from tissue specimens was assessed, taking composite reference standard (CRS) as reference standard. A total of 63 consecutive specimens of EPTB (June 2016 to May 2017), one showed the growth of non-tubercular mycobacterium on culture and was excluded from the study. Among the remaining 62 specimens, the most common were female genitourinary specimens (endometrial biopsies)- 30.64%, followed by vertebral tissue 29.03% and bone tissue 9.68%. The positivity shown by smear microscopy and HPE was 12.9% each, culture 14.52% and Xpert MTB/RIF assay 32.26%. The sensitivity and specificity of Xpert MTB/RIF assay in comparison to culture were 100% and 79.25% respectively. Whereas, CRS which includes smear microscopy, culture, histopathological, clinical and radiological findings, as reference standard, Xpert MTB/RIF assay showed sensitivity 64.52%, specificity 100%. This study suggests that Xpert MTB/RIF assay has good diagnostic potential for the rapid diagnosis of tuberculosis in tissue specimens, which could help in the timely initiation of antitubercular treatment and prevention of progression to irreversible changes.