Outbreaks of invasive disease caused by Neisseria meningitidis(Nm) have increased in the United States in the 1990s. Rapid DNA-based methods with greater ability than serogrouping to distinguishNm strains could be useful for evaluation of potential outbreaks. Rep-PCR, which can be completed in 24-48 h, uses primers based on conserved, extragenic repetitive sequences (elements) to generate DNA fingerprints of bacterial isolates. We sought to determine the ability of rep-PCR to identify outbreak-related Nm isolates and discriminate among Nm strains. Methods: Forty-three Nm isolates of serogroup B or C were studied: 8 were possibly related to an outbreak in Houston, TX in 1981; 12 were from Los Angeles, CA (collected in 1985-86 by the CDC); and 23 were from Spain (collected in 1985-86; 17 of these represented ET-5 complex isolates). These 35 had been evaluated previously by others using multilocus enzyme electrophoresis (MLEE). Two fingerprint sets were generated from genomic DNA samples by PCR using primers based either on the Ngrep or the BOXA repetitive sequences (derived from Neisseria spp. and pneumococci, respectively). DNA band patterns were made by agarose gel electrophoresis of PCR amplicons. Fingerprint analysis and dendrogram construction were performed in a blinded fashion. Results: Each rep-PCR fingerprint set allowed correct identification of the 7 outbreak-related isolates among the 8 in the outbreak set. Among the other 35 isolates, MLEE had identified 17 strains. Rep-PCR using the Ngrep- and BOXA-based primers delineated 14 and 13 strains, respectively. Rep-PCR grouped the isolates from Los Angeles and Spain into four and three clusters, respectively, that were identical to the groupings by MLEE.Conclusions: DNA fingerprints produced by rep-PCR allowed identification of outbreak-related isolates in a blinded set. The ability of rep-PCR to discriminate between strains of Nm was similar to that of MLEE. Rep-PCR holds promise as a rapid, genome-based typing method for delineation of apparent outbreaks of Nm disease caused by strains with serogroup B or C.