In this study, it was aimed to determine the DNA damage using the comet assay, which specifically shows DNA damage in naturally Babesia spp.-infected sheep and to evaluate the damage before and after imidocarb application. Blood samples obtained from 10 infected sheep with positive clinical signs and symptoms of babesiosis and whose diagnosis was confirmed by Giemsa staining and PCR methods, and blood samples from 10 healthy sheep were used as study material. DNA damage was examined by the comet assay from the blood samples of the infected patient group and the control group obtained during the disease and after the treatment, and the results were compared with statistical methods. When DNA damage was examined in sick animals diagnosed with babesiosis, the tail length and the tail moment values were found to be statistically significantly higher than the control group (P<0.0001). According to the results obtained after imidocarb application, it was determined that DNA damage and tail moment decreased statistically with imidocarb, and the difference was statistically significant, and the values were higher than the control group (P<0.0001). As a result, Babesia infection can cause DNA damage, has been confirmed by the determination of direct DNA damage using the comet assay, and imidocarb given for treatment was successful and reduced the damage.