Staphylococcus aureus is a major human pathogen harboring several virulence factors and super antigens (Sag) or staphylococcal enterotoxins (SEs). These factors are associated with the presence of agr (Accessory Gene Regulator) locus that controls the expression of several of them. We aimed to determine the prevalence of super antigens and agr groups in 151 methicillin resistant and sensitive S. aureus and to investigate possible relationships between them. A series of six multiplex PCR were conducted. Gradual increase in methicillin resistant S. aureus isolates was evident in this study. Additionally, steady decline in agr II, III and IV types with emergence of agr type I as predominant type was a significant feature. Seventy nine toxin genotypes were observed, with the most common genotype being sea-sek-seq. A meaningful relationship between the major toxin genes, methicillin resistance and agr type 1 was observed. Enterotoxin gene cluster (egc)1 was more common than egc2. The overall prevalence of virulence factors corresponds with that seen in other European countries; however preferential association in this study between agrI and sea-sek-seq combination may serve as efficient triggering signal of virulence in clinical S.aureus isolates.