Staphylococcus aureus, a major human pathogen, produces a wide array of toxins, which causes various types of disease symptoms. Prevalence of S. aureus in various foods collected during 2006-2008 in Korea was investigated. S. aureus was isolated from 275 of 5,186 (5.3%) food samples collected from hyper-markets in Korea. Seasonal temperature affected the prevalence of S. aureus in various foods with high isolation rate during the summer. Most of the enterotoxigenic strains produced enterotoxin A only or enterotoxin A in combination with another toxin. A total of 54.5% of the tested strains contained either one or more enterotoxin genes and 3.6% possessed a tst gene. This study offers basic information for securing the stability of food during storage and circulation, and provides an epidemiological tool to study the cause, origin and temporal spread of S. aureus food poisoning.