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Abstract Background Nosocomial infections due to vancomycin-resistant enterococci (VRE) have become a major problem during the last years. The purpose of this study was to investigate the economic burden of nosocomial VRE infections in a European university hospital. Methods A retrospective matched case-control study was performed including patients who acquired nosocomial infection with either VRE or vancomycin-susceptible enterococci (VSE) within a time period of 3 years. 42 cases with VRE infections and 42 controls with VSE infections were matched for age, gender, admission and discharge within the same year, time at risk for infection, Charlson comorbidity index (±1), stay on intensive care units and non-intensive care units as well as for the type of infection, using criteria of the Centers for Disease Control and Prevention. Results The median overall costs per case were significantly higher than for controls (EUR 57,675 vs. EUR 38,344; p = 0.030). Costs were similar between cases and controls before onset of infection (EUR 17,893 vs. EUR 16,600; p = 0.386), but higher after onset of infection (EUR 37,971 vs. EUR 23,025; p = 0.049). The median attributable costs per case for vancomycin-resistance were EUR 13,157 (p = 0.036). The most significant differences in costs between cases and controls turned out to be for pharmaceuticals (EUR 6030 vs. EUR 2801; p = 0.008) followed by nursing staff (EUR 8956 vs. EUR 4621; p = 0.032), medical products (EUR 3312 vs. EUR 1838; p = 0.020), and for assistant medical technicians (EUR 3766 vs. EUR 2474; p = 0.023). Furthermore, multivariate analysis revealed that costs were driven independently by vancomycin-resistance (1.4 fold; p = 0.034). Conclusions This analysis suggested that nosocomial VRE infections significantly increases hospital costs compared with VSE infections. Therefore, hospital personal should implement control measures to prevent VRE transmission.