Sequestration of spirochetes and concurrent histopathologic lesions were evaluated in tissues of Borrelia burgdorferi-infected dusky-footed woodrats (Neotoma fuscipes) and deer mice (Peromyscus maniculatus). Rodents were either wild-caught and naturally infected or were experimentally infected by tick bite, by intramuscular (i.m.) injection of cultured spirochetes, or by i.m. injection of tick suspensions. Samples of host tissues, including skin, blood, ear, brain, eye, heart, lung, liver, spleen, kidney, and urinary bladder, were removed from up to 21 woodrats and four deer mice and cultured in BSK II medium. Borreliae-positive cultures of ear punch biopsies were obtained from 10 of 11 woodrats and from all of four deer mice. Additionally, positive cultures were obtained from three of 36 skin biopsies of woodrats, and from one of 36 cultures of woodrat blood. In contrast, spirochetes were not observed in 505 cultures of internal organs or whole blood. Samples of tissues from seven naturally infected woodrats, four experimentally infected woodrats, and nine experimentally infected deer mice also were examined for histopathologic lesions. Nonsuppurative cellular infiltrates were recognized in samples from most tissue types from woodrats, but few lesions were observed in tissues from deer mice. Recognized lesions in woodrats that were consistent with infections of Lyme borreliosis in other species included synovitis, myositis, and myocarditis. Such lesions were more common in woodrats than in deer mice. Inflammatory lesions, especially synovitis, were more common in woodrats with long-term infections than in woodrats with relatively short-term infections. No clinical signs of disease were observed in either species of rodent.