Enterococci have recently been recognized as a causative organism of intractable infections, including severe sepsis and infective endocarditis, in immunocompromised patients. This study investigated the epidemiological, microbiological, and prognostic characteristics of high-level gentamicin-resistant (HLGR) enterococcal bacteremia, including severe cases of infective endocarditis, in Japan. A total of 155 enterococcal bacteremia episodes were identified between July 2007 and December 2009. HLGR strains accounted for 28% of all enterococcal strains: HLGR Enterococcus faecalis/Enterococcus faecium strains accounted for 32%/24%. The 30-day mortality rate was 31%. There was no significant difference in the 30-day mortality rates between HLGR and non-HLGR enterococcal bacteremia. There were two cases of HLGR enterococcal endocarditis, which were successfully treated with ampicillin plus ceftriaxone. We consider it important to examine the presence or absence of HLGR strains in all cases of intractable enterococcal infection, especially infective endocarditis.