Staphylococcus aureus (SA) is a species of the genus Staphylococcus that is found everywhere, including in the respiratory tract and on the skin of many adults and children, and that is considered one of the main pathogens in nosocomial and community acquired infections. The number of Methicillin-Resistant Staphylococcus aureus (MRSA) strains has increased globally over the past two decades. Determining the frequency of mecA gene in SA that represent MRSA in hospitalized children and comparing it upon hospital admission and discharge therefore appear essential. The present cross sectional study was conducted in children hospitalized in Imam Reza hospital in Kermanshah, Iran in 2012. Nasal specimens were collected from the 500 children at time of admission, considered as community acquired Staph aureus and those whose first nasal culture was negative were included for second culture at time of discharge, considered as hospital acquired Staph aureus. After identifying Staphylococcus aureus by common laboratory tests, methicillin resistance was determined using Oxacillin screening plates and mec -A gene. The prevalence of community acquired Staph aureus nasal carriers was estimated as 4.6% and the prevalence of its hospital-acquired type as 5.6%. The prevalence of mecA gene was 17/4% and 37% in two groups, suggesting no statistically significant differences between the two groups. The resistance to Erythromycin, Cefoxitin, Mupirocin and Clindamycin was 30/4%, 8/7%, 4/3% and 30/4% in the admission group and 40/70%, 7/4%, 7/4% and 18/5% in the discharge group, suggesting no statistically significant differences between the two groups. All the samples were sensitive to Vancomycin and Linezolid and no instances of resistance to these antibiotics were observed. The increase in the prevalence of MRSA is caused by the overuse of antibiotics, which facilitates the colonization of MRSA. Moreover, the increase in the resistance to commonly-used antibiotics is a warning for a more reasonable prescription of sensitive antibiotics such as Vancomycin, so as to prevent the emergence of multidrug resistant MRSA.