In Borrelia hermsii， antigenic variation occurs as a result of a nonreciprocal gene conversion event that places one of ~60 silent variable major protein genes downstream of a single， transcriptionally active promoter. The upstream homology sequence (UHS) and downstream homology sequence (DHS) are two putative cis-acting DNA elements that have been predicted to serve as crossover points for homologous recombination. In this report， a targeted deletion/in cis complementation technique was used to directly evaluate the role for these elements in antigenic switching. The results demonstrate that deletion of the expression site results in an inability of the pathogen to relapse in immunocompetent mice， and that the utilized technique was successful in producing complemented mutants that are capable of antigenic switching. Additional complemented clones with mutations in the UHS and DHS of the expressed locus were then generated and evaluated for their ability to relapse in immunocompetent mice. Mutation of the UHS and inverted repeat sequence within the DHS rendered these mutants incapable of relapsing. Overall， the results establish the requirement of the inverted repeat of the DHS for antigenic switching， and support the importance of the UHS for B. hermsii persistence in the mammalian host.