Reduced vancomycin susceptibility in Staphylococcus aureus can cause serious problems relating to treatment failure and persistent infection. We investigated vancomycin susceptibility, genetic relationships and transcriptional changes of the accessory gene regulator (agr) in vancomycin-intermediate S. aureus (VISA) strains isolated from South Korea compared with vancomycin-susceptible S. aureus (VSSA) strains. Molecular characterization, population analysis profiling, agr sequencing and transcriptional profiling of RNAIII by real-time RT-PCR were performed. Of 16 VISA strains tested, eight exhibited ST5, agr II and type II SCCmec. The others exhibited ST239, agr I and type III SCCmec. A point mutation in AgrA (Asp8Gly or Ile238Lys) was found in only five VISA strains; no mutations were detected in the other strains. However, RNAIII levels markedly decreased in all VISA strains (mean of 1.39-fold change) compared with the VSSA strains (31.51-fold change) in late-exponential phases (P<0.0001). The downregulation of RNAIII could be an important genetic event in the VISA strains, regardless of the presence or absence of the agr mutation.