A two-month-old Appaloosa colt developed neurological signs shortly after birth involving deficits affecting cranial nerves IV, VIl, Vil, IX, X and XII, and possibly nerve VI. The most likely differential diagnoses were congenital anomalies, meningoencephalitides, trauma or nutritional causes. The foal was investigated by the analysis of cerebrospinal fluid (CSF), electromyelography (EMG), brain auditory evoked responses, magnetic resonance imaging (MRI), peripheral nerve biopsy, and Western blot analysis for the presence of intrathecal antibodies to Sarcocystis neurona, the causative agent of equine protozoal myeloencephalitis. Significantly abnormal EMG findings included spontaneous electrical activity of the tongue, suggesting denervation. The MRI was useful in ruling out masses, congenital anomalies and focal abscessation. The cytology of CSF revealed mild mononuclear reactivity. Western blot testing of CSF was positive, indicating the intrathecal presence of antibodies to S neurona. The foal was treated with pyrimethamine and trimethoprim-sulphadiazine for two months and returned to nearly normal neurologic status.