The periplasmic flagellum of Borrelia burgdorferi consists of a unipeptide flagellar filament, a hook, and a basal body. Here, we report the cloning and expression of the hook gene,flgE, of B. burgdorferi N40. The flgE gene is 1,119 nucleotides long and is located on the 950-kb linear chromosome of B. burgdorferi. The primary protein sequence of FlgE shows 73% similarity to the FlgE protein of Treponema phagedenis and similar to 50% similarity to the FlgG proteins of both gram-positive and gram-negative bacteria. The flgE gene was cloned into an Escherichia coli expression plasmid, pMX, to produce FlgE protein. Subsequently, FlgE murine antiserum was prepared by immunizing mice with the partially purified B. burgdorferi FlgE protein. By Western blot (immunoblot) analysis, the antiserum was found to react with a 40 kDa peptide in the whole-cell lysates, confirming the expression of the flgE gene in B. burgdorferi. Additionally, antibodies to FlgE were found in serum specimens from 19 of 42 patients,vith Lyme disease. Moreover, when other antigens, including 41G (the immunodominant domain of flagellin), OspE, OspF, and p22, were used to test for the development of corresponding antibodies in these patients, 67% of these patients (28 of 42) reacted to at least one of these five antigens, suggesting that a combination of FlgE with other available B. burgdorferi recombinant proteins is a goad candidate for substrates in assays to aid in the diagnosis of Lyme disease.