Results of national and international surveillance studies revealed increasing rates of vancomycin-resistant Enterococcus faecium (VREF) among German hospital patients since 2003. To investigate the molecular background of vanA-type glycopeptide resistance, 51 clinical VREF isolated between 2004 and 2006 and originating from 19 German hospitals representing 10 Federal States have been investigated. Isolates were characterised by multi-locus sequence typing (MLST), SmaI macrorestriction analysis in pulsed-field gel electrophoresis (PFGE), and multiple-locus variable-number tandem repeat analysis (MLVA). Phylogenetic relatedness between strains was identified using BioNumerics and eBURST software. Distribution of virulence markers esp and hyl(Efm) was investigated by PCR. The structure of the vanA gene clusters was investigated by PCR, long-template PCR, sequencing and Southern hybridisations. The 51 VREF were rather diverse constituting different strain types, different virulence markers and vanA clusters. Within this diversity we found supportive data for a dissemination of related--already vancomycin-resistant--E. faecium among various hospitals and Federal States and for spread of identical vanA gene clusters among clonally different strain types within single hospitals. In conclusion, the increase in the rates of VREF among German hospital patients within the last 2 years might be rather complex and due to different molecular events and scenarios.