Failures in the antibiotic therapy of Lyme disease have repeatedly been demonstrated by post-treatment isolations of the infecting borreliae. Analyses of the antibiotic susceptibility patterns of borreliae may help to understand the causes of such treatment failures and to develop new therapeutic regimens.The three subspecies of Borrelia burgdorferi known to be pathogenic for humans and to differ in their virulence and organ affinity possibly may also show divergent susceptibilities to some common antibacterial agents. In order to get real clues for such probable differences we compared the efficacy of six antimicrobial agents against 24 borrelial tick and skin isolates belonging to the three subspecies of B. burgdorferi sensu lato.In five comparative evaluations, some significantly different antibiotic sensitivity of the three borrelial species was found. The Borrelia burgdorferi sensu stricto isolates showed lower sensitivity to cephalosporin, tetracycline and ciprofloxacin as well as a higher sensitivity to erythromycin compared to the B. afzelii and B. garinii isolates. The B. garinii isolates proved to be more sensitive to penicillin in comparison to the B. burgdorferi s.s. and B. afzelii isolates.In the light of these data, treatment failures may be interpreted by serum and tissue levels of the antibiotic too low for an effective killing of the infecting Spirochetes. However, prolonged treatment regimens applying higher dosages of antibiotics, in order to get complete clearing of the infection, may be linked to aggravated side effects.Therefore, the combination of different antiborrelial agents with synergistic effect seems to be a meaningful alternative and should be included in future studies in vitro as well as in vivo.