Recent studies demonstrated that mortality associated with methicillin-resistant Staphylococcus aureus (MRSA) bacteremia was high when vancomycin was used to treat infections with strains that had a high vancomycin minimum inhibitory concentration (MIC). This study compared several characteristics of vancomycin MIC 2 μg/ml strains isolated from bacteremia with those isolated from infections other than bacteremia. A total of 128 episodes of MRSA bacteremia between 2005 and 2008 were followed-up, and compared with 631 MRSA infections other than bacteremia. The isolation of strains with a 2 μg/ml MIC accounted for 32.0% of isolates from MRSA bacteremia, whereas strains with a 2 μg/ml MIC comprised 9.0% of MRSA isolated from other sites (p < 0.001). The incidence of pneumonia as the source of infection was significantly higher in patients with bacteremia from strains with a 2 μg/ml MIC than in those with ≤1 μg/ml MIC. Prior vancomycin use did not correlate with the isolation of 2 μg/ml strains. The efficacy of glycopeptides as 1st line therapy in patients infected with 2 μg/ml strains was significantly lower than that for patients infected with ≤1 μg/ml strains (30.0 vs. 78.8%, p < 0.001) in bacteremia. In the analysis of infections other than bacteremia, efficacy did not reveal a significant difference according to MIC (69.0 vs. 79.6%, p = 0.109). In bacteremia, mortality was 65.8% in patients with 2 μg/ml strains and 19.5% in patients with ≤1 μg/ml strains (p < 0.001), whereas there was no significant difference in mortality from infections other than bacteremia (10.7 vs. 7.8%, p = 0.617). In multivariate analysis, bacteremia with 2 μg/ml strains, intensive care unit (ICU) stay, and liver cirrhosis were independent risk factors for death in patients with bacteremia, and initial appropriate therapy lowered the risk. Several characteristics such as a higher incidence than at other infection sites, a high incidence of pneumonia as a source of infection, a low success rate of vancomycin therapy, and poor prognosis were confirmed in 2 μg/ml MIC MRSA isolated from bacteremia; however, a low success rate of vancomycin and poor prognosis were not apparent in 2 μg/ml MIC MRSA strains isolated from infections other than bacteremia.