Multiple sclerosis (MS) is a demyelinating, autoimmune, degenerative disease of the central nervous system (CNS). About 80% of MS patients have cerebellar symptoms consisting of tremors, impaired motor control, and coordination. Major aspects of Cerebellar dysfunctions are due to changes in Purkinje neurons. There is a critical need to elucidate the pathophysiology and mechanism of these symptoms. To understand this pathophysiology, we focused on energy production changes in demyelinated and damaged axons. This was achieved by investigating the role and changes in mitochondria activity of Purkinje cells in the cerebellum of an animal model of MS, experimental autoimmune encephalomyelitis (EAE). This model recapitulates axon demyelination, inflammation, and neurodegeneration of the CNS, as seen in MS. I hypothesize an increase in mitochondrial dysfunction plays a significant role in cerebellar pathology. To test this hypothesis, we conducted a longitudinal EAE cerebellum study. Cerebellar brain sections from EAE mice 21, 40, and 60 days post-induction were immunostained with myelin basic protein (MBP) and microglia specific (Iba-1), purkinje cells specific (calbindin) antibodies. Mitochondria activity in the molecular layer and Purkinje cell layer was also investigated by staining with Cytochrome Oxidase Subunit IV antibody (CoxIV). CoxIV catalyzes the final step in the mitochondrial electron transfer chain and is regarded as one of the significant regulation sites for oxidative phosphorylation. On Day 21, after peak EAE disease, there was a decrease in MBP expression, an increase in Iba-1, and a trend with increased COXIV expression. Day 40 of EAE showed decreased MBP and increased COXIV activity compared to normal, and Day 60 EAE showed decreased MBP and increased Iba-1 with no difference in COXIV activity compared to normal. We also conducted electron microscopy on EAE Day 40 Purkinje axons to investigate axon damage and mitochondrial morphology, which showed increased axonal damage and changes to mitochondria morphology. These data demonstrate mitochondria dysfunction at peak disease following irreversible axon damage.