The performance of an automated DNA amplification assay (Roche Cobas Amplicor Mycobacterium Tuberculosis Test (aPCR) was compared with an in-house single tube nested polymerase chain reaction (nPCR) for the direct detection of Mycobacterium tuberculosis in respiratory specimens. Among 385 specimens, 56 were culture positive for mycobacteria (44 positive for Mycobacterium tuberculosis and 12 positive for non-tuberculosis mycobacteria). The diagnostic sensitivities of aPCR and nPCR were 86% and 91% whereas a 100% diagnostic specificity of both assays was attained. By aPCR, inhibitors were detected in 6% of the clinical samples. For nPCR, the usage of a new thermostable DNA polymerase facilitated pre-PCR decontamination using uracil-N-glycosylase and "hot start" in single step procedure. The results of the study indicated that DNA amplification assays, either manual or automated, were rapid and specific tools for diagnosing pulmonary tuberculosis.