Background: Eimeria is a genus of protozoan parasites that infect many animal species, including horses. We conducted a cross-sectional study of indigenous breeds of horses from the North and Northeast of Iran to establish the prevalence and distribution of Eimeria species. Material and methods: Using standard coprological techniques, 340 faecal samples from randomly selected horses (141 from North Iran and 199 from Northeast Iran) were examined for Eimeria oocyst. Results: Out of 340 samples, only three from north Iran were positive for coccid- iosis. Infections occurred by Eimeria leuckarti. The mean intensity of oocyst output (3–38 o.p.g.) was very low. No clinical signs of gastrointestinal disorders were noticed in horses during this study. Conclusion: In conclusion, the results of this study suggest that the prevalence of Eimeria species causing coccidiosis in indigenous breeds of horses from the North and Northeast of Iran is relatively low. These findings provide valuable insights into the health status of indigenous horses in Iran and may help guide future efforts to promote their welfare and productivity.

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