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<p>Abstract</p> <p>Background</p> <p>Nucleic acid amplification assays including PCR have revolutionized the detection of <it>Mycobacterium tuberculosis </it>(MTB). Tuberculosis spread to almost every organ of the body and is characterized on the basis of localization of infection. Therefore, different types of body fluids and tissues can be used for the detection of MTB.</p> <p>From 2004 to 2010 total 766 different types of smear negative samples from patients, clinically suspected for tuberculosis were received and investigated at Division of Molecular Diagnostics, University of the Punjab Lahore for the diagnosis of tuberculosis. <it>Mycobacterial </it>DNA was extracted followed by PCR amplification.</p> <p>Findings</p> <p>A total of 356 (46.5%) samples were found positive by PCR for MTB. These included; serum (4.8%), blood (36.3%), urine (46.6%), cerebro spinal fluid (CSF) (42.1%), ascetic fluid (67.6%), pleural fluid (52%), pericardial fluid (30%), pus (38.6%), bone marrow (60%), sputum (38.8%) and bronchoalveolar lavage (BAL) (70%). Over all there was no significant difference in males and females neither in different age groups for the identification of MTB.</p> <p>Conclusion</p> <p>We conclude that PCR is a useful and sensitive tool for the early diagnosis of MTB in variety of clinical samples.</p>