Out of twenty rabbits which died of rabbit hemorrhagic disease spontaneously occurring in Korea, five animals had a concurrent infection with Encephalitozoon cuniculi in the cerebrum. The lesions were composed of granulomas, leptomeningitis and perivascular cuffing with mononuclear cells. The granulomas consisted of a central necrotic focus surrounded by an infiltration with plasma cells, lymphocytes and macrophages. Gliosis was associated with the granulomas. Gram-positive organisms were detected in the cerebrum from two rabbits. They were oval to rod-shaped with blunt round ends. The distribution of the pathogens was investigated by the direct avidin-biotin peroxidase complex method. They were present in pseudocysts and macrophages. Pseudocysts were found in the granulomas as well as the neuropil without cellular reactions. Some organisms were present within reticulo-endothelial cells of blood capillaries and macrophages in the subarachnoid spaces. These organisms had ultrastructural characteristics consistent with Encephalitozoon cuniculi.