This cross-sectional study was conducted from November to December of 2013 at the Cayetano Heredia National Hospital in Lima, Peru, to determine the rate of infection with vancomycin-resistant enterococcus (VRE), the resistance genotype, and associated factors. The rate of infection with VRE was 6.2% (95% confidence interval [CI]: 1.67–10.73) and the resistance genotype isolated from all strains was the vanA gene. The factors associated with colonization with VRE were previous hospitalizations (p = 0.001) and the use of third-generation cephalosporins (p = 0.016). In conclusion, perianal colonization with VRE is present in many hospital services. Moreover, the vanA gene may cause resistance to vancomycin and promote the development of vancomycin-resistant Staphylococcus aureus. Therefore, infection control measures should be adopted to prevent the dissemination of this bacterial strain in hospital settings.