Infection of susceptible mice with Theiler's murine encephalomyelitis virus results in neurological dysfunction from progressive central nervous system demyelination that is pathologically similar to the human disease, multiple sclerosis. We hypothesized that the development of neuropathology proceeds down a final common pathway that can be accurately quantified within a single spinal cord lesion. To test this hypothesis, we conducted quantitative ultrastructural analyses of individual demyelinated spinal cord lesions from chronically infected mice to determine whether pathological variables assessed within a single lesion accurately predicted global assessments of morphological and functional disease course. Within lesions we assessed by electron microscopy the frequencies of normally myelinated, remyelinated, and demyelinated axons, as well as degenerating axons and intra-axonal mitochondria. The frequency of medium and large remyelinated fibers within a single lesion served as a powerful indicator of axonal preservation and correlated with preserved neurological function. The number of degenerating axons and increased intra-axonal mitochondria also correlated strongly with global measures of disease course, such as total lesion load, spinal cord atrophy, and neurological function. This is the first study to demonstrate that functional severity of disease course is evident within a single demyelinated lesion analyzed morphometrically at the ultrastructural level. The role of axonal injury in the development of permanent neurological dysfunction is an important focus of research studying central nervous system (CNS) demyelinating diseases in humans. Multiple sclerosis (MS) is the most common CNS demyelinating disease in humans, 1 and recent studies describing the extent of axonal injury in MS lesions have stimulated new interest in the role of axonal loss in long-term neurological disability during the course of this disease. 2,3 Despite the numerous reports of axonal pathology in MS patients, axonal damage after chronic demyelination is not completely understood. Therefore, the study of axonal loss in animal models of demyelinating disease may aid in the understanding of disease pathogenesis and the development of potential treatment strategies.Theiler's murine encephalomyelitis virus (TMEV) causes a chronic progressive demyelinating disease in susceptible strains of mice that is pathologically indistinguishable from MS. 4 -9 Intracerebral injection of TMEV into mice of the prototypic susceptible background (SJL/J) results in a biphasic disease characterized by an acute neuronal polioencephalitis followed by chronic white matter demyelination and neurological deficits. 10 Twenty-one days after postinfection, viral persistence is observed in oligodendrocytes, not neurons, and therefore, should not contribute directly to progressive neuronal disruption. 11,12 During the chronic phase of disease, multifocal demyelinating lesions are primarily localized to the white matter of the brain stem and spinal cord, and th...