Staphylococcus aureus is the most common cause of skin and soft tissue infections in the community and the most important cause of nosocomial infections. In this research, it was aimed to detect the presence of staphylococcal enterotoxin A to D (SEA, SEB, SEC and SED, respectively), toxic shock syndrome toxin-1 (TSST-1), Panton-Valentine leukocidin (PVL) and SCCmec phenotype in methicillin-resistant S.aureus (MRSA) isolates and to demonstrate the genotypic association between hospital acquired and community acquired isolates. In the study the virulence factors of 147 S.aureus strains isolated from various clinical samples at Gulhane Military Medical Academy Hospital Microbiology Laboratory between 2007 and 2010 were investigated by real-time polymerase chain reaction. MLVA (multiple locus variable number of tandem repeat analysis) method was used to demonstrate the genotypic association between hospital-and community-acquired isolates. Seventy-two (%48.9) of 147 S.aureus isolates were determined as community acquired and 75 (%51.1) as hospital acquired. Ninety-three (63.2%) isolates possesed at least one toxin (77 strains harboured one, and 16 strains harboured more than one). Of the isolates in which toxin was detected 59.1% (55/93) were hospital acquired, 40.9% (38/93) were community acquired. SEA was determined in 59 (40.1%), SEB in 8 (5.4%), SEC in 12 (8.1%), SED in 8 (5.4%), TSST- 1 in 17 (11.5%) and PVL in 6 (4.0%) of the isolates. Methicillin resistance was determined in 61.1% (44/72) of the hospital acquired isolates and 6.7% of the (5/75) community acquired isolates. In our study, SCCmec type III was detected in 90.9% (40/44) of hospital acquired MRSA isolates and SCCmec type IV in 40.0% (2/5) of community acquired MRSA isolates. Most of the strains (40/47; 85.1%) carrying SEA were hospital acquired, and they were determined as methicillin-resistant. According to MLVA, hospital and community acquired groups' clustering rates, number of clones, number of unique profile were determined as; 73.6% and 57.3%; 34% and 47%; 19% and 32%, respectively. It was concluded that high prevalence of SEA toxin in hospital acquired MRSA isolates indicated that there was a possible association between the presence of toxin and antimicrobial resistance.