Background: We aimed to determine molecular characteristics ofStaphylococcus aureusisolates cultured from hospitalized pediatric patients. Methods: All accessibleS. aureusisolates cultured from hospitalized pediatric patients were analyzed for staphylococcal cassette chromosomemec(SCCmec) types, Panton-Valentine Leukocidin (PVL) encoding genes and antibiotic resistance patterns. Results: A total of 132S. aureusisolates, 102 methicillin-susceptibleS. aureus(MSSA) (81.8%), 30 methicillin-resistantS. aureus(MRSA) (18.2%) were included in the study. Sixty of 132 (45.5%)S. aureusisolates were cultured from skin and soft tissue infections (SSTIs), 50 (37.9%) from bloodstream infections, 11 (8.3%) from bone infections and 11 (8.3%) from other sterile sites. Fifty-three of 102 (52%) MSSA isolates were cultured from SSTI, 35 (34.3%) from bloodstream infections, 7 (6.9%) from bone infections and 7 (6.9%) from other sterile sites (P= 0.083). Fifteen MRSA isolates (50%) were cultured from blood culture, 7 from (23.3%) SSTI, 4 (13.3%) from bone infections and 4 from (13.3%) other sterile sites. Nine PVL gene harboringS. aureusisolates were isolated from SSTI (75%), 2 from blood culture (16.7%) and 1 from other sterile site (8.3%). Three MRSA (6.7%) isolates were found to be positive forSCCmectype III and 16 MRSA isolates (53.3%) were found to be positive for SCCmectype IV. Three MRSA isolates harboring SCCmectype III was isolated from blood culture, 11 of 16 MRSA isolates harboring SCCmectype IV was isolated from blood culture, 3 isolates were isolated from bone infections and 2 isolates were isolated from SSTI (P< 0.001). Five of 72 (6.9%) hospital-acquiredS. aureusisolates and 7 of 60 (11.7%) community-acquiredS. aureusisolates were PVL gene positive. Twenty-two of 72 (30.6%) hospital-acquiredS. aureusinfections and 8 of 60 (13.3%) community-acquiredS. aureusisolates were MRSA (P= 0.015). All of the 3 SCCmecIII harboring MRSA isolates and 11 of 16 SCCmecIV carrying MRSA isolates were hospital acquired. Hospitalization in the past 1 year was found to increase MRSA infections 3.95 times (P= 0.038, 95% confidence interval: 1.078-14.48). Conclusions: As distribution of virulence genes differs amongS. aureusisolates from different regions, it is necessary to monitor the emergence of genes encoding PVL, SCCmecin both MRSA and MSSA throughout the world. Our results show a high prevalence of PVL in community-onsetS. aureusinfections in children.SCCmectype IV was more commonly isolated in hospital-acquired MRSA isolates, and PVL gene was more commonly isolated in community-acquiredS. aureusinfections.