Neuronal ceroid lipofuscinosis (NCL) is an inherited, neurodegenerative disorder with fatal outcome in humans. It has also been described in some animal species; this is the first report of NCL in equines. Three horses showed developmental retardation, slow movements and loss of appetite at the age of six months. Neurological symptoms, as well as visual failure in one case, were noticed at the age of 1 year. Due to slowly progressing deterioration, euthanasia was indicated 1.5 years after onset of conspicuous behavior. At necropsy, slight flattening of the gyri and discoloring of the brain was noticed. Histopathology revealed eosinophilic, autofluorescent material in the perikarya of neurons throughout the brain and spinal cord. Identical material was found in neurons of retina, submucous and myenteric ganglia, as well as in glial cells. Immunohistochemistry, using antiserum against subunit c of mitochondrial ATP synthase, showed positive signals in neurons and glial cells. Electron microscopical studies revealed fingerprint profiles mixed with rectilinear structures in markedly enlarged lysosomes of neurons and renal tubules, and rectilinear structures mixed with curvilinear bodies in macrophages and lymphocytes of lymph nodes. Thus, our study presents the first occurrence of lysosomal storage disease in horses, further characterized by immunohistochemical and electron microscopical investigations as NCL.