The purpose of this study was to evaluate Mycobacterium tuberculosis complex isolates recovered from clinical specimens with culture methods with an automatized polymerase chain reaction (PCR) method. Specimens sent to the mycobacteriology laboratory were decontaminated and concentrated with the standard NaOH-NALC method and then cultured on Löwenstein-Jensen solid medium and BACTEC B12 vials containing Middlebrook 7H12 broth. Fourty-one specimens with typical colonies on Löwenstein-Jensen medium and 127 specimens identified as M. tuberculosis complex in radiometric BACTEC system (Becton Dickinson Diagnostic Instruments Systems, Cockeysville, MD, USA) were marked as the study group. As control group 46 specimens without growth on either culture media were selected. The results of 32 (78.1%) specimens grown on Löwenstein-Jensen media were positive with COBAS AMPLICOR MTB PCR (Roche Diagnostic Systems, Inc., Branchburg, NJ, USA) method whereas 86 (67.8%) of specimens identified in BACTEC system were positive with COBAS AMPLICOR MTB PCR method. All (100%) culture negative specimens within the control group were also negative with COBAS AMPLICOR MTB PCR method. It is concluded that although it is a rapid method in the identification of M. tuberculosis complex isolates from clinical specimens, COBAS AMPLICOR MTB PCR method is less sensitive than culture and that it can only be used together with the culture technique.