The aims of the work presented here were to evaluate a commercial system based on DNA hybridization technology on nitrocellulose strips (GenoType MTBC; Hain Diagnostika, Nehren, Germany) for identifying Mycobacterium tuberculosis complex isolates to the species level and to compare the results with those obtained using the RFLP-PCR and multiplex PCR molecular techniques, biochemical tests and susceptibility testing. The commercial system correctly identified 102 of 103 (99.03%) strains studied, indicating it is capable of discriminating among the tuberculosis complex species.