Efferent lymph and peripheral blood collected from sheep experimentally infected with Toxoplasma gondii strain S48 were analysed for parasite DNA by amplification of the B1 and P30 T. gondii genes by the polymerase chain reaction (PCR). The relative sensitivity of these two gene amplification methods was assessed and compared with parasite detection by mouse injection (MI). B1 PCR was consistently more sensitive than P30 PCR and the results agreed closely with those from MI. By contrast, P30 PCR gave more than twice as many false negatives results than B1 PCR. The few apparent false positive results given by either PCR method were probably due to the inability of MI to detect non-viable parasites. All specimens collected before infection with T. gondii gave negative results by PCR and MI. Parasite DNA was detected by both B1 and P30 PCR in the lymph node of a sheep 12 days after infection but not in other tissues. The results permit a direct comparison between T. gondii detection by P30 and B1 PCR. Moreover, they further confirm the value of PCR detection of toxoplasma as a sensitive, specific and reliable diagnostic and research tool.