This study was carried out to determine the prevalence and pathology of coccidiosis in goats in the Khartoum State, and the influence of age, sex and oocysts load on the infection rate. A hundred faecal samples were directly collected from the rectum during September – December 2018, from goats rearing industry in Khartoum state .The animals were grouped according to sex and age group. Oocysts were detected using the floatation method; the Mc Master method was used for oocysts count. Length, width and size were measured by calibrated microscope attached to computer for the parasite identification. On the other hand, 100 samples of intestines were collected for gross and microscopic examination, from Albaraka slaughterhouse in Omdurman. The gross intestinal lesions were reported and sections for histopathology were made according to standard methods. The results revealed that the overall prevalence was 79%.Eimeria species identified were: E.ninakohlyakimovae, (41.6%). E. aspsheronica (16%), E. caprovina (16%), E.christenseni (12.5%), E. hirci (8%), E. jolchijevi (4%).According to age, adult goats had significantly lower prevalence than kits. However, kits expressed significantly higher mean of oocyst loud, while adults showed lower means of oocysts loud .The study indicated that no significance difference between male and female infection. The macroscopic examination revealed white scattered nodular lesions of coccidiosis observed from the external surface of the affected areas, along with thickening of the intestinal mucosa. Microscopic examination revealed different developmental stages of Eimeria are found filling all epithelial cells of the villi with sloughing and destruction of the villi. Coccidiosis in goats was found high in Khartoum State. Kids are more susceptible to infection. It is recommended that the proper management is necessary for control of coccidiosis and the animals should be separated according to the age group to avoid the infection.