The prevalence of Eimeria in 50 examined rabbits was 84% (42/50). The prevalence was 92.6% in male rabbits while it was73.9% in female rabbits. According to age, the prevalence was determined 88% in rabbits less than 4 months of age while it was 80% in rabbits 4 months of age or more. No significant difference was recorded between rabbits in correlation to age and sex. Ten species of Eimeria infecting rabbits were isolated in Assiut by parasitological examination. The prevalence of Eimeria species were E. perforans (66.7%) followed by E. exigua (26.2%), E. media (26.2%), E. magna (21.4%), E. intestinalis (19%), E. coecicola (19%), E. irresidua (19%), E. piriformis (14.3%), E. flavescens (7.1%) and E. stiedae (7.1%). Single infection of Eimeria spp. was found in 23.8% of the infected rabbits, where as mixed infection involved two, three or four Eimeria spp. was observed in 76.2% of the infected rabbits. Clinical signs were depression, anorexia, diarrhea while postmortem examination revealed hepatomegaly with presence of separate yellowish-white nodules of varying sizes spread over the surface with distended gall bladder. The intestinal lesions revealed varying degree of congestion, thickening of intestinal wall. Histopathological examination of the liver revealed dilated bile ducts and formation of papilliform projections of epithelium containing different developmental stages of Eimeria, associated with degeneration and pathological changes in hepatic parenchyma. The intestinal coccidiosis revealed hyperplasia of the epithelial cells and presence of Eimeria oocytes and gametocytes within the epithelial cells of the villi associated with lymphocytic infiltration in the lamina propria of the villi. The transmission electron microscope showed asexual and sexual developmental stages of rabbit Eimeria including developing schizont and macrogametocyte.