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A disease with clinical manifestations of thickening and alopecia of the skin over the lower limbs, around the eyes, face, and nose, thickening and shrinkage of the scrotum, and presence of white granular cysts in the sclero-conjunctiva in goats in Kerman Province, were reported to the Pathology Department of Shiraz Veterinary School. Primary histopathological studies demonstrated an outbreak of caprine besnoitiosis in this region. To study the histopathological and ultrastructural features of the disease, samples were collected from various organs of the suspected slaughtered goats for further investigations. In histopathological studies, dermis and subcutaneous fascia covering lower portion of the limbs, skin over frontal sinus, ear tips, scrotum, eye lids as well as the eye's sclera, epididymal and testicular parenchyma, and their tunics were severely infected with Besnoitia cysts. Tongue, pharynx, prepuce and penis, deeper striated muscles, subcutaneous bone matrices, abomasum, esophagus, subcutaneous tendons, and periosteal surfaces of the limb bones showed lower rates of infection. Except the vagina and vestibule, no cyst was observed in other female urogenital organs, the central nervous system, intestines, heart, liver, spleen, and different lymph nodes. The host reaction to the cysts was variable, ranging from the absence of inflammatory cells around intact normal cysts up to infiltration of macrophages, lymphocytes, plasma cells, eosinophils, fibroblasts, and connective tissues around the degenerated cysts. Ultrastructural studies showed this coccidian parasite belonged to eukaryotic protozoa, and the cystic form had the typical feature of the Besnoitia spp. of the apicomplexa. This study showed that the organism demonstrated ultrastructurally minor differences with other Besnoitia species infecting other animal species.