Molecular techniques were used to study the epidemiology of infections due to Enterobacter aerogenes in a tertiary-care hospital. Sixty-two clinical isolates were collected from 43 patients over 3 months. Restriction endonuclease analysis (REA) of chromosomal DNA and repetitive-element polymerase chain reaction (rep-PCR) with primers based on repetitive extragenic palindromic (REP) and enterobacterial repetitive intergenic consensus (ERIC) bacterial DNA sequences were used for genomic fingerprinting. REA with HindIII or EcoRI yielded complex banding patterns that differentiated community-acquired from some hospital-acquired organisms. Less complex fingerprints were obtained with rep-PCR, which also distinguished between epidemiologically unrelated strains. More discriminatory DNA fingerprints were provided by rep-PCR when REP primers rather than ERIC primers were used. Two clusters of genomically distinct isolates from patients with recent or current exposure to the hospital environment were identified by REA and rep-PCR. Most isolates within each cluster contained characteristic plasmids, and some isolates contained additional plasmids. These results suggest colonization and infection with genotypically related strains of E. aerogenes in a nosocomial setting. Although REA and plasmid profiling are useful techniques for the epidemiological typing of E. aerogenes, genomic fingerprinting with rep-PCR may offer the advantages of ease, speed, and broad species applicability over existing molecular-typing techniques.