Background:Staphylococcus aureus is amongst major human pathogens both in hospitals and the community. This bacterium is an opportunistic pathogen responsible for a large number of self-limiting and even life-threatening diseases in humans. Methicillin resistant S. aureus (MRSA) strains are common causes of emerging nosocomial infections and are considered as a major problem for public health.Objectives:We aimed to study the profile of some virulence genes including: sea, seb, sed, tst, eta, etb, LuKS/F-PV, hla and hld in methicillin-resistant S. aureus by the PCR technique.Materials and Methods:A total of 345 isolates of S. aureus were collected from clinical specimens of patients referred to teaching hospitals of Shiraz; identification was done by biochemical (catalase, coagulase and DNase) and molecular tests. One hundred and forty six isolates of methicillin-resistant S. aureus (MRSA) were obtained and the presence of some toxin genes in these isolates was investigated by the polymerase chain reaction (PCR) technique.Results:The results showed that among the 345 isolates of S. aureus, 148 were confirmed as MRSA by screening with the cefoxitin disc diffusion (30 µg) method. Also among the 148 MRSA isolates, 146 isolates were confirmed as methicillin-resistant by molecular methods. The results showed that the frequency of methicillin-resistant and methicillin-sensitive S. aureus isolates during 2012 to 2013 in Namazi and Faghihi hospitals were 146 (42.3%) and 199 (57.7%), respectively. Besides, among the 146 confirmed MRSA isolates, 36.98% (54 isolates) and 63.02% (92 isolates) were related to female and male, respectively. The largest number of cases belonged to sputum samples (58 out of 146). The frequency of the eta, etb, sed, LuKS/F-PV, seb, tst, sea, hld and hla genes were 0.68%, 2.05%, 2.05%, 5.47%, 10.95%, 11.64%, 27.39%, 84.24% and 93.15%, respectively. In addition, amongst all examined genes, hla (93.15%) and eta (0.68%) genes had the highest and lowest frequencies, respectively. The greatest coexistence of genes was observed for the hla + hld gene combination (48.83%). The results of our study indicate that 98.63% of the isolates were positive for at least one of the virulence genes.Conclusions:The relative higher frequency of some virulence genes in this study may reflect the emergence of isolates containing these genes in Shiraz medical centers.