The Lyme disease spirochete, B. burgdorferi is atypical in that a large portion of its genome is in the form of plasmids. Many of the plasmid-carried genes form extensive paralogous gene families and encode outer-surface proteins. In this report we have assessed the humoral immune response to proteins belonging to the paralogous protein family, family 163. We have cloned and expressed BBP39, BBO40, BBQ47 and BBN39 and used these recombinant proteins to monitor the temporal nature of the antibody response to these antigens during experimental infection of mice. The immunodominant regions of each protein have also been assessed through immunoblot analyses of a series of truncations of each protein. These analyses have led to the delineation of the targets of the antibody response during infection and of the specificity of the antibody response to family 163 proteins. In addition, we quantified the expression of each gene using real time RT-PCR.