OBJECTIVE: To evaluate by species-specific immunoblots the association of Borrelia burgdorferi sensu stricto, B. garinii and B. afzelii with neuroborreliosis in Switzerland. METHODS: Borrelia strains isolated from the cerebrospinal fluid (CSF) of three children with neuroborreliosis were typed by phenotypic and genotypic analysis. The serologic reactions (IgG) of these three patients as well as those of 28 patients, including one of these three children, with confirmed neuroborreliosis were characterized and scored by immunoblots on the three individual Borrelia species antigens. Twenty patients with typical erythema migrans served as a control group. RESULTS: Phenotypic and genotypic analysis confirmed that all three CSF isolates were B. garinii. In the 28 patients with neuroborreliosis, the comparatively strongest reactions were as follows: 18 to B. garinii, three to B. burgdorferi sensu stricto and two to B. afzelii; five were inconclusive. In the control group (erythema migrans), the comparatively strongest reactions were as follows: six B. garinii, one to B. burgdorferi sensu stricto and five to B. afzelii; eight were indeterminate. CONCLUSIONS: Typing of these three CSF isolates and characterization by immunoblots of the antibody reactions of patients with neuroborreliosis give additional evidence of the association of B. garinii and neuroborreliosis. Our serologic results suggest that B. burgdorferi sensu stricto and B. afzelii are also responsible for some neuroborreliosis cases in Switzerland. Our immunoblots and the scoring system proved particularly useful for the serologic typing of patients with late Lyme borreliosis.