The presence of granuloma, visualized in histopathology for diagnosing tuberculosis in tissue samples, is not a specific finding. Moreover, histopathological examination of tissue sections needs one to two weeks for final reporting. A rapid and sensitive method is therefore needed for detection of Mycobacterium tuberculosis in these paucibacillary tissue samples.A PCR-assay specific for IS6110 was evaluated for 104 different tissue samples in comparison to histopathology that was considered gold standard.PCR showed 74.1% sensitivity and 96.1% specificity. False positive and false negative results were observed in three (2.88%) and seven (6.73%) samples, respectively. Positive agreement between histopathology and PCR was observed as 0.737, indicating substantial good agreement between two tests.PCR can be used for early diagnosis of tuberculosis in tissue samples that can help to initiate timely anti-tubercular treatment and prevent progression to irreversible changes.