This invention relates generally to an assay for Lyme disease which detects the antibody to Borrelia burgdorferi, the causative agent of Lyme disease. More specifically, the assay employs antigens derived from amino acid regions in the flagellum of Borrelia burgdorferi. These antigens are immunoreactive with antibodies to Borrelia burgdorferi but are not substantially immunoreactive with antibodies to Treponema pallidum, the syphilis causing agent. DNA sequences of the antigens, clones and vectors containing the DNA sequences are also disclosed. Polypeptides derived therefrom can be used as reagents for the detection of antibody to Borrelia burgdorferi in the body fluids from individuals with Lyme disease.