Background and Objective: Staphylococcus aureus is one of the few bacteria that can infect all body organs The aim of this study was to compare the reliability of the cefoxitin disk diffusion method with other phenotypic and molecular methods in detection of methicillin-resistant S. aureus (MRSA). Furthermore, this study was designed to determine the relative prevalence of MRSA and its antibiotic susceptibility in clinical specimens of admitted patients in Ahvaz educational hospitals. Materials and Methods: A total of 693 S. aureus isolates were collected from clinical specimens of Ahvaz hospitals. Detection of MRSA strains was performed using Oxacillin disk diffusion, Oxacillin screening agar, cefoxitin disk diffusion and PCR. The S. aureus susceptibility test was also performed by disk diffusion and vancomycin agar screening methods. Results: 0ut of a total of 693 specimens, 280 specimens were confirmed as S. aureus. A number of MRSA, 121 (43. 2%) strains by Oxacillin disk diffusion, 122 (43. 5%) strains by Oxacillin screening agar, 123 (43. 9%) were identified by cefoxitin disk diffusion and PCR. The results of antibiotic susceptibility pattern showed the highest resistance toward the erythromycin (98. 3%), followed by ciprofloxacin(97. 5%), clindamycin (94. 3%), tetracycline (90. 2%), gentamicin (83. 7%) and rifampin (41. 4%) were noticed. On the other hand, the least resistance was observed against teicoplanin (0%), linzolide (0%), and vancomycin (0%). Conclusion: The prevalence of MRSA in our region was relatively high, but these strains were totally sensitive to vancomycin, teicoplanin and linzolide antibiotics. Cefoxitin disk test is a reliable method for detection of MRSA strains.