Enterococcus faecium has recently emerged as a serious nosocomial pathogen. The emergence of multiple antimicrobial agent-resistant E. faecium has been remarkable; with its strains it is one of the most phenotypically heterogeneous of all enterococcal species. About 15% of enterococcal strains isolated from human clinical specimens were found to have atypical biochemical characteristics. In order to determine if these strains were E. faecium variants, intergenic ribosomal polymerase chain reaction (ITS-PCR) and E. faecium PCR (EfPCR) were performed in 45 atypical strains, and the two PCR results were used to analyze phenotypic characteristics of the strains. As many as 60% (27/45) of the atypical strains were identified as E. faecium. Thus, it is concluded that if an enterococcal strain shows positive reaction to arabinose, arginine, and ribose and negative reaction to methyl-alpha-D-glucopyranoside and pigment, it should be identified as E. faecium.