Characterization of the host immune response during initial pathogenesis of relapsing fever neuroborreliosis would be a key to understanding Borrelia persistence and factors driving the inflammatory process. We analyzed immune cells in brain and kidney with the highly invasive B. crocidurae during the first two weeks of murine infection. In both organs, microglia and/or macrophages predominated while T-cell changes were minimal. Compared to kidney, brain neutrophils infiltrated more rapidly and B-cells were essentially absent. Our results indicate that during early neuroborreliosis, brain defense is comprised primarily of innate immune cells while adaptive immunity plays a minor role.