To evaluated the PCR for mecA gene compared with the conventional oxacillin disk diffusion method for methicillin-resistant Staphylococcus aureus (S. aureus) identification. A total of 292 S. aureus strains were isolated from various clinical specimens obtained from hospitalized patients. Susceptibility test to several antimicrobial agents was performed by disk diffusion agar according to Clinical and Laboratory Standards Institute guidelines. The PCR amplification of the mecA gene was carried out in all the clinical isolates. Among antibiotics used in our study, penicillin showed the least anti-staphylococcal activity and vancomycin was the most effective. The rate of methicillin-resistant S. aureus prevalence determined by oxacillin disk diffusion method was 47.6%; whereas, 45.1% of S. aureus isolates were mecA- positive in the PCR assay. This study is suggestive that the PCR for detection of mecA gene is a fast, accurate and valuable diagnostic tool, particularly in hospitals in areas where methicillin-resistant S. aureus is endemic.