The present investigation was carried out to study the prevalence of Staphylococcus aureus and its antimicrobial resistance pattern isolated from various types of human clinical infections. One hundred and fifty clinical specimens were collected from the educational hospitals of Iran. Samples were cultured and those that were S. aureus-positive were confirmed using the PCR. Antimicrobial resistance pattern was analyzed using the disk diffusion method. Of 150 samples studied, 50 samples (33.33%) were positive for S. aureus. The results of the culture method were confirmed using the PCR amplification of 16S rRNA gene of the S. aureus. Burn infections had the highest prevalence of S. aureus (40%). S. aureus strains of our study harbored the highest levels of resistance against penicillin (94%), tetracycline (92%), oxacillin (90%) and azithromycin (80%). Keep the skin and especially wound and burn infections clean away from the polluted environment of hospitals and regular prescription of imipenem, methicillin and vancomycin may be good instructions to reduce the risk of S. aureus infections in the cases of human clinical infections.