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One hundred twenty-nine Slovenian isolates of Borrelia burgdorferi sensu lato derived from patients (69 strains) or Ixodes ricinus ticks (60 strains) were characterized. All of the strains were first- or second-passage isolates obtained in 1992 and 1993 from the same endemic region. The techniques used for the molecular analysis of strains included species-specific polymerase chain reaction (PCR) typing, and pulsed-field gel electrophoretic separation of undigested and MluI-digested genomic DNA. Isolates were identified to the species level by large restriction fragment pattern (LRFP) analysis and the results compared with the species-specific PCR result. Fifty-two patient isolates (75%) were typed as Borrelia afzelii (LRFP MLa1), 6 (9%) as Borrelia garinii (LRFPs MLg1-4), and 11 (16%) as Borrelia burgdorferi sensu stricto. The latter included 9 isolates (13%) with a new LRFP that is not typical of Borrelia burgdorferi sensu stricto and for which the designation MLx is suggested. In contrast, only 32 of 60 (53%) tick isolates were typed as Borrelia afzelii, while 20 strains (33%) were typed as Borrelia garinii and 8 strains (13%) as Borrelia burgdorferi sensu stricto. Three new LRFPs were found among the Borrelia garinii (MLg5 and 6) and Borrelia burgdorferi sensu stricto (MLb15) tick isolates. Large restriction fragment pattern analysis identified new groups of Borrelia burgdorferi sensu lato and revealed an apparent difference in the isolation frequency of different species from patients and ticks in the same endemic region.