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Resistance to methicillin in methicillin resistant Staphylococcus aureus (MRSA) is dependent on mecA gene located on staphylococcal cassette chromosome (SCC). Both SCCmec type and Panton-Valentine leukocidin (PVL) affect S. aureus pathogenicity. Aim of this study was to investigate the prevalence of SCCmecA types and pvl genes among MRSA isolates from inpatients. During this cross-sectional study on 100 clinical isolates, following antibiotic susceptibility test, screening of mecA and pvl genes, as well as SCCmec typing, was done in a multiplex PCR technique. From the studied samples, 58 isolates were recognized as MRSA. The frequency of mecA and pvl was 58% and 4%, respectively. All of the MRSA were resistant to cefoxitin and had the highest sensitivity to chloramphenicol. The majority (77.5%) of MRSA was originated from wound samples. The SCCmec III was the most frequent type (22.4%) in these samples. The pvl positive isolates were from SCCmec IVb and V, thus meaning they are from CA-MRSA. These results show a high prevalence of MRSA in the studied region and a widespread prevalence of SCCmec I-V types. Furthermore, high prevalence of SCCmec III indicates the prevalence of multidrug resistant MRSA. This finding is a serious alarm for medical health care practitioners for the correct use of antibiotics in order to limit the spread of multidrug resistant strains. In addition, with regard to life threatening infections caused by pvl harbouring strains, early diagnosis and treatment of infections caused by these isolates should be mandatory.