The prevalence of vancomycin-resistant Enterococcus faecium (VRE) infection at a medical center in eastern Taiwan rose to 80.6%, exceeding the average prevalence of 55.6% among all medical centers nationwide during the same period. In recent years, the number of cases of VRE infection detected among hospitalized patients has increased annually. However, most of these patients in different wards are asymptomatic carriers. Therefore, restricting active screening to high-risk units will not improve the current situation, and it is necessary to review the risk factors for VRE colonization to provide a reference for future infection control policies. Between 2014 and 2019, there were 3,188 VRE-positive cultures reported at our institution, per the electronic medical records system (EMR). In the medical and surgical wards, patients who received penicillin (odds ratios: 2.84 and 4.16, respectively) and third-generation cephalosporins (odds ratios: 3.17 and 6.19, respectively) were at higher risk of VRE colonization. In intensive care units, the use of carbapenems (odds ratio: 2.08) was the most significant variable. This study demonstrated that the risk factors for VRE colonization differed between wards. Thus, policies should be established according to the attributes of patients in each ward, and active screening tests should be performed according to individual risks, instead of a policy for comprehensive mass screening.