Clinical, clinicopathological macroscopical and histopathological findings, as well as electron microscopic and cultural confirmation, in twelve natural cases of canine encephalitozoonosis are described, eleven of these under one year of age. Nervous symptoms, including blindness, retarded growth rate and nephritis are prominent clinical signs. The macroscopic findings and histopathology proved of great help in the diagnosis of the disease even in chronic cases. The organism was cultured and some distinguishing electron microscopical features between Encephalitozoon and Nosema are discussed. A transmission experiment confirmed the diagnosis. The results are compared with the reported cases in dogs and Blue Foxes (Alopex lagopus).