The methicillin-resistant Staphylococcus aureus (MRSA) colonization rate was determined in children grades K to 3 in 7 Minnesota schools during the 2004/2005 and 2006/2007 school years. Seven (0.9%) were colonized with MRSA in 2004/2005 and 3 (0.5%) were colonized with MRSA in 2006/2007. Although the MRSA colonization rate did not change, a higher percentage MRSA nasal colonization isolates were community-associated MRSA strains in 2006/2007.