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S. aureus is reported as a major cause of nosocomial infections after dental care and involved in endocarditis, bacteremia, osteomyelitis, peritonitis, and soft tissues etc. It is very important to identify the distribution and the diversity of toxin gene associated with the S. aureus expression in dental care patients with periodontitis directly for an effective prevention and treatment of dental diseases. Fifty four strains of S. aureus were isolated from the saliva of 129 patients who were diagnosed with periodontitis at dental clinics and hospitals located in Seoul. The distribution of the virulence gene and the genetic diversity of the strains were studied using the polymerase chain reaction with isolated strains. The enterotoxin test showed Seb was the most frequent gene with 88.9%. The hemolysin gene of Hla, Hib and Hld were the most frequently gene with 98.1% (53 strains), leukocidins gene of lukM showed 90.7% (49 strains), and laminin binding protein gene of Eno showed 100% (54 strains), respectively. The diversity of the enterotoxin gen was held as Seb-Seg-Sei gene of 35.2% (19 strains), the diversity of hemolysin gene of Hla-Hlb-Hld gene was 98.1% (53 strains) and the diversity of leukocidins gene of LukD-LukM were 88.9% (48 strains), respectively. Patients with dental disease showed somehow high toxin gene expression so that S. aureus in dental care area is judged to show very highly pathogen with a high and infection rate. In the future, additional studies for these toxin genes seem to be required.