West Nile Virus produces lesions in the gray matter of the mid-brain, hind-brain, and spinal cord. Lesions tend to increase in severity the closer they are to the hindquarters. Lesions can be symmetrical or asymmetrical, effecting both or only one side of the horse. They can also be in more than one location, so combinations of clinical signs may vary.

Equine Protozoal Myeloencephalitis, or EPM, is one of the most common neurological diseases affecting the horse. Most horses exposed to the causative organism, Sarcocystis neurona, will clear any infection with their own immune system. However, in horses with a compromised immune system, the organism can spread to the central nervous system causing a very serious and debilitating disease.