An increasing number of clonal outbreaks caused by members of the E. cloacae complex is being reported. For the detection of clonality, pulsed-field gel electrophoresis (PFGE) is considered the golden standard, but PCR-based methods are cheaper, easier to perform, and provide faster results. One hundred ninety-five isolates of the E. cloacae complex isolated at the university hospital Grosshadern, Munich, Germany, were assigned to their respective genetic cluster by partial hsp60 sequencing. All study isolates belonging to genetic clusters III and VI were selected to evaluate the specificity of the enterobacterial repetitive intergenic consensus (ERIC) and repetitive extragenic palindromic (REP) polymerase chain reaction (PCR) for the identification of clonal isolates belonging to the E. cloacae complex. For these 56 isolates, PFGE was performed, yielding 3 pairs of isolates with indistinguishable patterns. ERIC PCR resulted in 7 groups with identical patterns, together encompassing 49 study isolates. Comparing the ERIC PCR with the PFGE, a specificity of 14% considering the detection of "clonal" isolates was calculated. In this respect, REP PCR performed much better, yielding a specificity of 90%. An unweighted pair-group method with arithmetic averages tree based on ERIC PCR patterns allowed an accurate classification of the isolates to the respective genovars, suggesting that the ERIC PCR differentiates between genovars rather than between strains. In contrast, REP PCR differentiates better on the strain level. A proposed diagnostic system for the detection of subsumed outbreak strains of the E. cloacae complex is presented. It is based on an initial REP PCR, which should be confirmed by PFGE in cases of identical patterns, whereas ERIC PCR does not seem to be useful for the detection of outbreak strains when dealing with isolates of the E. cloacae complex.