Rapid diagnosis is critical for treating and preventing infections due to vancomycin-resistant enterococci (VRE). We assessed the performance of GeneOhm VanR and Xpert vanA/vanB assays that detect vanA and vanB, the two most important genes encoding vancomycin resistance, utilizing 50 stool samples from renal dialysis patients, as well as well-characterized VRE strains. Stool samples were screened for the presence of VRE by culture followed by polymerase chain reaction (PCR) for the detection of van genes in isolates. Furthermore, the direct detection of vanA/vanB from aerobically and anaerobically pre-enriched stools was performed by in-house PCR sequencing. GeneOhm was less sensitive (43.5% vs. 73.9%) and more specific (100% vs. 92.6%) than Xpert in detecting vanA from stool samples. vanB detection by GeneOhm was more sensitive than Xpert (100% vs. 87.5%), but equally non-specific (20.6% vs. 14.7%). A further estimation on log-serial dilutions of VRE strains showed that Xpert was more sensitive at detecting VRE at low concentrations (10-100 colony forming units [cfu]/ml).