Genes for flagellin A (FlaA) proteins from European borrelial strains of Borrelia burgdorferi sensu stricto, B. afzelii, and B. garinii were cloned and sequenced. An identity of 92 to 93% was observed in the flaA sequences of the different species. Polyhistidine-tagged recombinant FlaA (rFlaA) proteins were produced in Escherichia coli and used as antigens in Western blotting (WB) and enzyme-linked immunosorbent assay (ELISA). In immunoglobulin G (IgG) WB, 71% (10 of 14) of the sera from neuroborreliosis and 86% (12 of 14) of those from Lyme arthritis patients reacted with one to three rFlaAs. In IgG ELISA, 74% (14 of 19) and 79% (15 of 19) of patients with neuroborreliosis and arthritis, respectively, were positive. The immunoreactivity in local European patient sera was stronger against rFlaA from B. garinii and B. afzelii than against rFlaA from B. burgdorferi sensu stricto. Neither IgG nor IgM ELISA was sensitive in the serodiagnosis of erythema migrans. Serum samples from patients with syphilis and systemic lupus erythematosus showed mild cross-reactivity in IgG tests. Sera from Yersinia enterocolitica or beta-hemolytic Streptococcus infections showed only occasional responses. With IgM ELISA, 58% (11 of 19) and 37% (7 of 19) of patients with neuroborreliosis and arthritis, respectively, were positive. Cross-reactive antibodies to FlaA, especially in serum samples from patients with rheumatoid factor positivity and Epstein-Barr virus infection, reduced the specificity of IgM serodiagnosis. Therefore, rFlaA seems to have a limited role for IgM serodiagnosis, yet rFlaA might be useful in the IgG serodiagnosis of disseminated Lyme borreliosis.Laboratory diagnosis of Lyme borreliosis (LB) is mainly based on serology, although the present serologic tests have unsatisfactory sensitivity and specificity (34). Routine laboratory testing uses enzyme-linked immunosorbent assays (ELISA) with borrelial whole-cell lysate (WCL) or flagella (consisting mainly of polymerized FlaB protein) as the most commonly used antigens. A two-step approach with ELISA followed by a confirmatory Western blot (WB) has been recommended for positive or borderline results (19,36). Especially in Europe, the applicability of this procedure has, however, remained doubtful (3, 14) because three or more borrelial species cause LB (38). Several difficulties complicate LB serology. Firstly, immunoglobulin G (IgG) antibody responses are often delayed during the early stages of LB. Even at late-stage LB, 5 to 10% of patients do not have elevated antibody levels (29), perhaps due to diversion of the host immune response towards Th1 immunity by borrelial factors (17). Secondly, viral infections cause false-positive IgM results in several LB tests (4). Thirdly, in a subgroup of patients antibody levels may stay high after successful treatment of LB even for prolonged periods (6, 15).Several recombinant borrelial antigens (OspA, OspB, OspC, OspE, OspF, p22, BmpA, BBK32, BBK50, VlsE, p100, 14-kDa internal flagellin fragment) (5,7,16,21,22,24,25,31,35) and...