We detected the expression of outer surface proteins OspA and OspB, and characterized the genes encoding the two Osps of eight Borrelia garinii isolates from patients in Japan. Six of the eight strains shared a common antigenic epitope in their OspA and/or OspB proteins to monoclonal antibody P3134 against OspB, and were identified to have a conserved carboxyl terminus on their ospA and ospB genes by Southern blot hybridization. One strain, JEM4, did not express OspB protein, which was due to lack of the ospB gene. Gene cloning and sequencing analysis revealed that it had only one osp open reading frame with 819 nucleotides, which was similar to the ospA gene. The deletion of the ospB gene could be explained by a homologous recombination based on the common C-terminal sequences on the ospAB operon.