Invasive and skin community-associated (CA)-methicillin-resistant Staphylococcus aureus isolates from children were matched with invasive CA-methicillin-sensitive S. aureus strains during 2000-2004. Isolates were analyzed for presence of Panton-Valentine leukocidin. A USA400 lineage clone (n = 6) and the predominant USA300 lineage clone emerged.