Equine protozoal myeloencephalitis (EPM) was clinically diagnosed in a 20-year-old horse with severe ataxia. The cerebrospinal fluid was positive for Sarcocystis neurona antibodies by western blot. The horse was administered corticosteroids to facilitate in vitro culture of S. neurona from its spinal cord following necropsy. Microscopic lesions of EPM were present in the brain and in the spinal cord, including multifocal inflammatory cellular infiltrates and several large groups of protozoa. Immunohistochemical, and light and electron microscopic examinations revealed that the protozoa were Neospora caninum and not S. neurona. The protozoa divided by endodyogeny, tachyzoites had rhoptries, and organisms reacted specifically to N. caninum antibodies. Veterinarians should be aware of increasing diagnosis of N. caninum as another etiological agent responsible for the lesions of EPM.