The reliability of the Diversi-Lab System, an automated method of microbial strain typing using repetitive sequence-based polymerase chain reaction (rep-PCR), was evaluated by comparing results with those obtained by pulsed-field gel electrophoresis (PFGE). Ninety-five clinical isolates of vancomycin-resistant enterococci (VRE; 13 groups, 2-17 isolates per group) sent to Associated Regional and University Pathologists (ARUP) Laboratories for typing were tested by both methods. Rep-PCR and PFGE results were concordant for 83 isolates: all 32 isolates in 6 of the groups and 51 of the 63 isolates in the other 7 groups. Clustering of the remaining 12 isolates differed. With the Diversi-Lab System, analysis is objective, and results are available in 4 h, compared with a more subjective analysis and a 2- to 3-day turnaround time for PFGE. The Diversi-Lab System may be a viable alternative to PFGE for typing VRE in clinical reference laboratories.