Borrelia burgdorferi (Bb) enters the human body via the bite of an infected Ixodes tick. Lyme disease symptoms arise from the dissemination of Bb from the initial bite site to the distal tissues such as the heart, the joints, or the nervous system. We identified a novel Bb infectivity gene, bbk13, that is important for distal tissue colonization in a mouse model of infection. Detailed characterization of the infection kinetics showed that there is a critical Bb population expansion that occurs at the skin during early infection and that bbk13 is important for this process. This study highlights the significance of early spirochete expansion in the skin towards driving downstream events that lead to distal tissue colonization. Therapeutic approaches that limit the early, localized expansion in the skin may prevent the onset of disseminated Lyme disease symptoms.