Correct and rapid detection of methicillin resistance in Staphylococcus aureus is very important for treatment of infected patients. Detection of the mecA gene or PBP2a by polymerase chain reaction (PCR) is considered the gold standard for determination of methicillin resistance in staphylococci. In most clinical laboratories, phenotypic methods are used for the detection of methicillin resistance in S. aureus because PCR is not suitable for routine usage. In this study, we aimed to compare different phenotypic methods: disk diffusion, agar screening, latex agglutination and an automated system employed to establish the presence of methicillin-resistant S. aureus (MRSA). Presence of the mecA gene via PCR was used as the marker for MRSA positivity. Afterward, 214 samples were analyzed for methicillin resistance via oxacillin or cefoxitin disk diffusions, oxacillin agar screening, MRSA latex agglutination and the automated BD Phoenix system. Sensitivity, specificity, negative and positive predictive values of these phenotypic methods were evaluated. In the detection of MRSA, the cefoxitin disk-diffusion method was found to be more useful than oxacillin disk diffusion. The automated MRSA strain-detection system was found to be more successful than the other phenotypic methods. These results showed that the automated system could be used safely for routine MRSA detection.