Methicillin-resistant Staphylococcus aureus (MRSA) is well known to be a causative pathogen of skin and soft tissue or blood stream infections, and also to be a nosocomial drug-resistant bacteria in healthcare settings. Although a rapid and accurate detection of MRSA is indispensable for infection control, the conventional tests including culture method have some problems of sensitivity, procedure time, and so on. We evaluated the performance of the rapid detection assay of MRSA (BD GeneOhm MRSA Detection Kit) directly from specimens by a real-time PCR. The principle of this kit is characterized by recognizing not a mecA gene, but a specific part of SCCmec gene. Limits of detection of this method was 810 CFU/mL. Compared to the results of mecA PCR assay in 105 clinically isolated samples, the sensitivity, specificity, positive predictive value and negative predictive value were 100%, 97.4%, 98.5% and 100%, respectively. One of the 38 mecA negative isolates was found to be a positive result, this finding suggested that this method detect sequences of SCCmec/orfX region lacking of mecA. Because of the rapid turn-around time and the excellent negative predictive value, this method appears to be a useful tool for rapid diagnosis of MRSA.