Toxoplasma gondii and Neospora caninum are obligate intracellular protozoan parasites that can affect different warm-blooded species worldwide. In this study, it was aimed to detect T. gondii and N. caninum using PCR method in brain tissues of aborted sheep fetuses. Brain specimens were collected from 50 Morkaraman sheep fetuses that had undergone abortion at various stages of pregnancy, within the lambing seasons of 2023 in Muş. Approximately 1 cm³ of brain tissue from the right cerebral hemisphere was excised and subsequently frozen at -20°C for DNA extraction. DNA extraction and PCR amplification were then performed. As a result of this study, 11 (22%) of 50 brain tissues were positive. All brain samples examined in this study were negative for Neospora caninum. Based on the results of this study, it is possible to say that T. gondii is an important abortion agent in sheep in this region. Although N. caninum was not detected in this study, larger scale studies are recommended. Moreover, this study provides important information to breeders and veterinarians in the field in the evaluation and management of abortion.