Staphylococcus aureus is a major cause of infections in both hospitals and communities, and is exhibiting increasing resistance to methicillin (methicillin-resistant S. aureus, MRSA) and related beta-lactams. MRSA is usually considered a nosocomial pathogen, but increasingly it is acquired in the community. In Taiwan, MRSA was colonized in a substantial proportion of healthy children and accounted for 25% to 75% of childhood community-acquired (CA) S. aureus infections. From the preliminary data, the isolates of sequence type (ST) 59 by multilocus sequence typing method appeared to be the major clone of CA-MRSA in northern Taiwan. Compared with those reported from the US and other countries, CA-MRSA isolates in Taiwan did not always harbor type IV staphylococcal cassette chromosome (SCCmec) and were resistant to multiple non-beta-lactam antibiotics, including clindamycin and macrolides. Molecular evidence suggested transmission of the community strain of MRSA into the hospital setting, and that the community strain had became a health care-associated pathogen. The treatment of putative CA S. aureus infection should be stratified according to the severity and the disease entity.