Both tachyzoites and bradyzoites in tissue cysts of Neospora caninum are morphologically difficult to distinguish from those of other cyst-forming apicomplexan parasites such as Toxoplasma gondii. Thus, molecular tools may contribute to easy identification of the parasite. Based upon an N. caninum-specific DNA fragment that we have recently cloned, 5 sense (Np1, Np3, Np5, Np7, Np21) and 4 antisense (Np2, Np4, Np6, Np8) oligonucleotides were designed for a sensitive and specific polymerase chain reaction (PCR). Among 19 combinations of sense and antisense primers, the Np21/Np6, Np21/Np4, and Np7/Np6 primer pairs were found to generate specific single bands in the presence of at least 10 pg genomic parasite DNA as a template. The primer pair Np21/Np6 was able to detect a single tachyzoite in the background of DNA derived from 2 mg of brain tissue. In experimentally infected athymic ICR:nu/nu mice, N. caninum-DNA was detected consistently from brain tissue at days 13 and 18 after subcutaneous inoculation of tachyzoites. The presence or absence of the organisms in the cerebrum in either proliferative or cystic form was examined by immunohistological staining. The results indicate that PCR with the primer pair Np21/Np6 could provide an efficient tool for large-scale epidemiological studies using brain tissue obtained at necropsy.