This study was carried out to investigate Neospora caninum and Toxoplasma gondii tachyzoites in total of 400 whole peripheral blood samples with EDTA which were collected from the clinically healthy dogs in Kayseri region. Following the isolation of genomic DNA from the blood samples, spectrophotometric measurements of the obtained genomic DNAs were performed and appropriate concentrations were prepared for Real Time PCR (qPCR). qPCR analyses of the samples were conducted using the specific primers and probes that target the gene regions NC5 for N. caninum and RE for T. gondii. Out of 400 blood samples, 15 (3.8%) were found to be infected with N. caninum while no T. gondii positivity was determined in the examined samples. In conclusion, some molecular epidemiological data about N caninum and T. gondii infections dogs in Kayseri region were firstly demonstrated in Turkey with this study.