Methicillin-Resistant Staphylococcus aureus (MRSA) is responsible for an increasing number of serious hospital and community acquired infections. Virulence gene expression in Staphylococcus aureus is orchestrated by regulators such as the accessory gene regulator (agr). Staphylococcal strains are divided into four major agr groups (agrI-IV) on the basis of agrD and agrC polymorphisms. The purpose of this study was to define the prevalence of MRSA strains in appointed Tehran's hospitals and then to define and compare the proportion of agr I, II, III, IV polymorphisms between MRSA and Methicillin Sensitive Staphylococcus aureus (MSSA) strains. A total of 235 isolates were evaluated by conventional antibiotic susceptibility tests and PCR for agr and mecA genes. 112 strains were MRSA (47.5%) and the most prevalent agr specific group was agr I followed by agr III, agr II and agr IV, respectively. The prevalence of agr groups amongst MRSA and MSSA strains was not statistically significant (P>0.05). This study suggests that agr I is not only the most prevalent agr type in MRSAs but also the most common one in Methicillin Sensitive Staphylococcus aureus (MSSA) strains in Iran.