We have initiated a molecular approach towards understanding the basic biology and pathogenesis of the Lyme disease spirochete, Borrelia burgdorferi. Having cloned the genes for two major outer membrane proteins of the type strain, B31, on a single recombinant plasmid, we examined the organization of these genes on the original recombinant and in representative clinical and environmental isolates. Characterization of the recombinant plasmid has revealed that the genes for both of these abundant surface proteins are located in the right-most third of the spirochetal insert DNA and are transcribed in the same direction. Transposon Tn5 insertions within the region encoding OspA exert a polar effect on expression of OspB, indicating that these genes share a common promoter. DNA hybridization probes specific for Osp A and B of the type strain B31 have been prepared and used to examine the organization of these genes in several independent isolates of the Lyme disease borrelia.