Natural eastern equine encephalitis alphavirus (EEEV) infection was diagnosed in two adult horses with anorexia and colic, changes in sensorium, hyperexcitability, and terminal severe depression. Myocardium, tunica muscularis of stomach, intestine, urinary bladder, and spleen capsule had coagulative necrosis and perivascular lymphocytic infiltrate. Central nervous system (CNS) lesions were diffuse polioencephalomyelitis with leptomeningitis characterized by perivascular T lymphocyte cuffing, marked gliosis, neuronophagia, and multifocal microabscesses. Lesions were more prominent within cerebral cortex, thalamus, hypothalamus, and mesencephalon. EEEV was identified in the cytoplasm of cardiac myocytes and smooth muscle cells of spleen, stomach, intestine, urinary bladder, blood vessels, and dendritic cells. In the CNS, EEEV-positive cells included neurons, astrocytes, oligodendrocytes, microglia, and neutrophils. EEEV was isolated from the CNS of both horses. The detailed description of the encephalic and spinal EEEV localization and the findings of EEEV in extraneural tissues contribute to the understanding of this important multisystemic zoonotic disease.