VRE species are an increasingly important and universal problem in intensive care units and hematology-oncology departments due to the spread of glycopeptide resistance. Rapid and accurate identification of VRE is therefore crucial. The intent of this study was to compare the diagnostic performance of a real-time PCR test, the BD GeneOhm VanR assay (GeneXpert vanA/ vanB, Cepheid, USA), with conventional cultures for screening hospitalized immunocompromised hematology-oncology patients for VRE. Three hundred and six duplicate rectal swab specimens were obtained from 120 pediatric hematology-oncology patients. PCR and conventional culture-based studies were performed. One hundred and twenty patients, 46 female and 74 male, participated in the study. The mean age of the patients was 7.5±4.7 years. A total of 51 specimens from 306 samples were found to be positive for vanA or vanB. Mean turnaround time for PCR was 0.5±0.2 days. Compared to the culture method, the RT-PCR assay had an overall sensitivity of 91.8% (34/37) and a specificity of 93.6%. The positive predictive value and negative predictive value were 66.6% and 98.8%, respectively. This study demonstrates that RT-PCR is a suitable alternative to culture-based procedures for rapid and accurate identification of VRE in hematology-oncology patients, as the overall performance of PCR is comparable to that of a chromogenic agar-based culture method for VRE screening, especially for detection of VRE-negative patients.