We previously classified locally isolated strains of Borrelia burgdorferi by a restriction fragment length polymorphism analysis of total DNA, by DNA/DNA Southern Blot hybridization and by a hybridization with rRNA 16 + 23S from Escherichia coli [Cinco et al. (1993) Microbiologica 16:323-332] into three genetic groups which, according to the reference strains used, should correspond to the three species so far described as B. burgdorferi sensu stricto, B. garinii and B. afzelii. To find a simpler method for strain identification, in this study we analyzed the Italian strains and some strains identification, in this study we analyzed the Italian strains and some strains originating from other European countries, employing the species-specific 16S rRNA primers in the polymerase chain reaction technique (PCR) and some phenotypic markers like the B. afzelii-specific monoclonal antibodies and the battery of OspA-specific monoclonal antibodies which were reported to give a reactivity pattern correlated to the species [Wilske et al. (1993) J Clin Microbiol 31:340-350]. The PCR results confirmed those obtained previously by identifying the three groups as B. burgdorferi sensu stricto, B. garinii and B. afzelii; the reactivity patterns obtained with the monoclonal antibodies (mAb) also corresponded to those described as typical of the three species. We standardized the PCR technique to amplify a sample of crude template DNA obtained from a culture of 10(5) spirochetes.