BACKGROUND: The recently developed nucleic acid amplification methods may provide us with very sensitive, specific and rapid tests for the detection of M. tuberculosis. So the aim of this study was to compare the commercial Amplicor M. tuberculosis kit and our in-house polymerase chain reaction (PCR) with the conventional culture and direct AFB staining method. Materials and METHODS: Among the total of 2,340 clinical specimens, 1,314 sputum samples were tested for the presence of M. tuberculosis by Amplicor PCR and 1,026 sputum samples were tested by in-house PCR performing with resin matrix preparation and DNA extraction, synthesized primer pair, detection using agarose gel electrophoresis. RESULTS: One hundred-seventeen specimens were positive by Amplicor PCR, 105 were positive by in-house PCR, 185 were positive by culture. The sensitivity of the Amplicor PCR for all of the specimens and for smear-positive and smear-negative specimens was 92.9%, 97.9% and 88.2%, respectively after discrepant analysis. The sensitivity of the in-house PCR for all of the specimens and for smear-positive and smear-negative specimens was 80.0%, 93.6% and 65.5%, respectively after discrepant analysis. The specificity of the Amplicor PCR and in-house PCR for all of the specimens was 97.9% and 99.0%, respectively. CONCLUSIONS: Amplicor PCR was more sensitive than in-house PCR, but there was another problems such as high false positive rate and high cost. So PCR may certainly become very useful in microbiological laboratories if PCR method is selected according to the laboratory conditions.