BACKGROUND: Several large outbreaks have demonstrated the threat of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) in close-contact environments, such as occurs during training and quartering of military recruits training. In South Korea, which is a hospital or healthcare-associated MRSA prevalent area, military service is compulsory for all healthy young men. We surveyed and determined the extent of CA-MRSA colonization in the upper respiratory tracts of Korean military recruits. METHODS: The Korean military recruits who were enrolled in a military training facility from November 2004 to March 2005 were eligible for this study. Sputum or nasopharyngeal swap was obtained from randomly selected subjects who displayed upper respiratory tract symptoms. RESULTS: Of the 181 participants, 32 participants (17.7%) were colonized with S. aureus, and 12 participants (6.6%) were colonized with MRSA. Among the cases that were colonized with S. aureus, 37.5% (12/32) were colonized with MRSA. Antimicrobial susceptibility testing showed resistant patterns that were suggestive of the CA-MRSA strains for all of the MRSA isolates. CONCLUSION: This study of Korean military recruits found a great deal of showed MRSA colonization in them, and the antimicrobial resistant profile that was suggestive of a CA-MRSA strain. Further efforts to prevent the spread of MRSA infections and careful monitoring for CA-MRSA outbreaks are warranted, especially in a high risk group such as military recruits.