The current study was carried out to investigate the prevalence of Eimeria species among 75 diarrheic calves in Assiut Governorate. Oocysts of Eimeria spp. were found in 46.7% (35/75) of the examined fecal samples from diarrheic calves using light microscope and 88% (22/25) by using PCR. Very high significant difference of Eimeria infection was recorded in calves 3-6 months of age, 73.3% (22/30) and 1 week-3 months of age 28.9% (13/45). The prevalence of Eimeria spp. in calves with diarrhea showed the highest rate in summer (69.2%), followed by winter (36.4%), autumn (25%) and spring (7.7%). Eight species of Eimeria were isolated by parasitological examination. The prevalence of Eimeria spp. was E. zuernii (51.4%) followed by E. bovis (31.4%), E. alabamensis (31.4%), E. cylindrica (25.7%), E. subspherica (14.3%), E. canadensis (11.4%), E. ellipsoidalis (5.7%) and E. auburnensis (2.9%). Single infection of Eimeria spp. was found in 48.6% of the infected calves, whereas mixed infection involved two, three or four Eimeria spp. was observed in 51.4% of the infected calves. In conclusion, season and age of the calves were the most significant aspects connected with the possibility of infection with coccidiosis The PCR is a more reliable, sensitive and less time-consuming approach for diagnosis of Eimeria.