After the intradermal inoculation of mice with Borrelia burgdorferi, the antibody response, culture, and histology of blood and target organs were assessed and compared with results of a nested polymerase chain reaction (PCR) assay. Of 247 specimens of heart, brain, bladder, and blood, the tested concordance between the PCR and culture was 72%. In the 69 instances of discordance, the PCR was positive in 51 and the culture was positive in 18; thus, the PCR was concordant or more sensitive in 93% of the tested organs. In mice infected with 10 spirochetes, serology confirmed by Western blotting (immunoblotting) was more sensitive than either culture or PCR of brain, bladder, or heart specimens. The organs most commonly culture or PCR positive were the heart and bladder; the brain was infected in only 26% of the animals. DNA hybridization was helpful in confirming the PCR product as being specific and, in some cases, in demonstrating a positive product in the face of negative agarose gels. PCR was less sensitive than culture in detecting the presence of spirochetes in blood specimens, possibly because of the presence of blood inhibitors. We thus found a nested PCR assay, using primers from a genomic sequence, to be a valuable adjunct to serology and culture in the study of murine Lyme borreliosis. The assay confirmed that, after small numbers of spirochetes are injected intradermally, the heart and bladder, and less frequently the brain, are sites of persistence of the spirochetes.