Vancomycin-Resistant E. faecium (VRE) strains from clinical specimens were identified by conventional methods before. Following the phenotype-based identification, all strains were also identified using both BD Phoenix and VITEK MS bioMerieux System. Strains were typed with the Bruker MALDI-TOF MS system, pulsed field gel electrophoresis (PFGE) and 16S rRNA gene sequencing analysis and then the sensitivity compared for each. A cut off value of 850 assigned with Bruker MALDI-TOF MS system was found to give equal sensitivity to that of PFGE. Results obtained were compared with those of molecular typing. The main advantage of MALDI-TOF MS technology over the others was the much shorter analysis time which lasted only a few hours rather than days or a whole week. Also, the Bruker MALDI-TOF MS system was used for typing and compared with the gold standard method and this study is first to report the determined cut off level for typing of VRE strains.