Objective: This study was performed to evaluate and compare the sensitivity of Polymerase Chain Reaction (PCR) targeting the 529 base pair (bp) gene and B1 gene to detect Toxoplasma gondii DNA. Material and Methods: A total of 49 mice (Mus domesticus domesticus) were divided into 4 groups and they were infected with tachyzoites of T. gondii RH strain. Brain, liver, spleen and blood samples were obtained from infected mice at 24, 48, 72 and 96 hours following the onset of the infection. The extracted DNAs were amplified by using primers designed for the 529 bp gene and the B I gene. Results: Both PCR assays succeeded to detect T. gondii DNA in most mice after 24 hours of infection. For each sample type, 529 bp gene PCR was more sensitive than B1 gene PCR in detecting T. gondii DNA (McNemar p < 0.05). The smallest number of tachyzoites, that Toxo DNA could be detected by B1 and 529 bp repeat gene PCR assays was 1 x 10(4) tachyzoites/mL and 1x 10(2) tachizoites/mL respectively, by using DNAs from serial tachizoite dilutions. Conclusion: For the diagnosis of toxoplasmosis in mice, 529 bp PCR was more sensitive than B1 PCR to detect T. gondii DNA.