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Infection with Borrelia burgdorferi was associated with encephalitis in a horse. The horse lived in an area of Wisconsin endemic for B burgdorferi infection. Borrelia burgdorferi was isolated from the brain, but rabies virus was not detected in the brain. Serum obtained from the horse had a B burgdorferi antibody titer of 1:2,048, but was negative for antibodies to eastern and western encephalomyelitis.