The importance of heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA) as a preceding stage for the development of vancomycin-resistant S. aureus is growing. We analyzed the prevalence of hVISA among bacteremia with methicillin-resistant S. aureus (MRSA) using two Etests and evaluated the clinical characteristics and outcomes. Ninety-eight MRSA isolates from blood were collected at two University hospitals in Korea. Macrodilution Etest and glycopeptide resistance detection Etests were used for detection of hVISA. Staphylococcal cassette chromosome mec (SCCmec) typing was performed by multiplex PCR. Clinical data were collected retrospectively from patient medical records. About 30% of MRSA strains were identified as hVISA. Diabetes mellitus was associated (P = 0.047) with hVISA infections. The hVISA isolates were associated with high teicoplanin MIC and multidrug resistance (P = 0.001). SCCmec type II accounted for the majority (79.3%) of hVISA strains. The prevalence of hVISA strains was increased and can lead to the development of multidrug-resistant strains. Patients with diabetes were found to have a greater risk for infection with hVISA strains. As the impact of hVISA on clinical outcome is not yet clear, large-scale studies about clinical outcomes and optimal detection methods of hVISA are needed. In conclusion, hVISA strains have a high prevalence in bloodstream MRSA infections. Awareness of the increase in hVISA strains should motivate laboratories to establish a system to detect and monitor hVISA.