The serodiagnosis of early Lyme neuroborreliosis is hampered by false negative results and one of the reasons could be the heterogeneity of strains of Borrelia burgdorferi sensu lato. For this study IgG enzyme-linked immunosorbent assays (ELISAs) with recombinant internal flagellin fragments (p41/i; amino acids 129-251) derived from strains PKo (B. afzelii), B31 (B. burgdorferi sensu stricto), and PBi (B. garinii) and ELISAs with whole-cell detergent extracts of strains PKo, PKa2 (B. burgdorferi sensu stricto), and PBi were compared. Cut off absorbance values were defined by the 94th and 92th percentiles of 200 sera from blood donors. Sera from patients with clinically defined neuroborreliosis [n = 88; 41 culture proven and 47 intentionally selected by the criteria specific IgG cerebrospinal fluid/serum index > or = 2 and a serum IgG immunofluorescence assay value of < 1:64] were tested. The sensitivities of the three whole-cell detergent-extract ELISAs were similar (46.6-49.2%), whereas those of the recombinant ELISAs were highest with p41/i:PBi (57.1%) and lowest with p41/i:PKo (21.5%). A combination of the p41/i:PBi and the p41/i:B31 test was most sensitive (59.8%). The correlation of absorbance values of different assays was very high for the three whole-cell detergent-extract ELISAs, whereas the absorbance values obtained with the three recombinant tests differed considerably. The greatest differences were observed between p41/i:PKo and any of the other two recombinant antigens. The differences in immune reactivity of patients sera (due to strain heterogeneity?) seems to have more influence on the results of an assay based on a single antigen than on a whole-cell-based test.