We investigated the prevalence and the molecular characteristics of vancomycin-intermediate Staphylococcus aureus (VISA) among methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from clinical samples at tertiary or general hospitals participating in a nationwide surveillance program for VISA and vancomycin-resistant Staphylococcus aureus (VRSA) in Korea during an 8-week period in each year from 2001 to 2006. Of 41,639 MRSAs isolated, 37,856 were screened and 169 grew on brain heart infusion agar supplemented with 4 microg/ml vancomycin. A vancomycin MIC of 4 microg/ml was confirmed for 33 VISA isolates of the 169 isolates. Eighteen of the 33 isolates were classified as hetero-VISA (hVISA) by the population analysis profile (PAP) method. All VISA isolates were susceptible to linezolid, tigecycline, and quinupristin-dalfopristin. Most VISA isolates (MIC 4 microg/ml) showed a PFGE C pattern with sec, seg, and sei enterotoxin genes, including ST5-SCCmec type II, or a PFGE A pattern with sea, including ST239-SCCmec type III.