Disseminated tuberculosis with negative pulmonary findings is a diagnostic problem, Histopathological studies of bone marrow (BM) and liver (LV) biopsies are the most reliable methods for diagnosis in such cases; however, their sensitivity is Limited. In this retrospective study, 41 BM and 7 LV paraffin-embedded biopsy specimens from clinically (clinical response to antituberculous treatment after 6 months follow-up) and/or histopathologically diagnosed tuberculosis were analysed for the detection of Mycobacterium tuberculosis DNA by polymerase chain reaction (PCR). Two different primer sets, one based on the repeated IS6110 sequence of M. tuberculosis and the other based on the mtp40 gene region, were used for amplification. Histopathological and PCR studies were positive for M. tuberculosis in 12/41, and 30/41 in BM and 4/7, and 6/7 in LV biopsy specimens, respectively. As the control group, 17 BM biopsy specimens obtained from patients with a positive Mantoux skin test but no active tuberculosis were analysed. One BM biopsy out of 17 control cases was positive with PCR while none was consistent with TB histopathologically. In conclusion, PCR might be applicable and more reliable than histopathological studies for detection of tuberculosis in BM and LV biopsy specimens.