Axonal pathology is a key contributor to long-term disability in multiple sclerosis (MS), an inflammatory demyelinating disease of the central nervous system (CNS), but the mechanisms that underlie axonal insults remain unclear. While most axonal pathologies characterized in MS are a direct consequence of myelin loss, we propose that axonal pathologies also occur independent of demyelination. In support of this idea, we recently reported that mice that develop experimental autoimmune encephalomyelitis (EAE), a model commonly used to mimic the pathogenesis of MS, exhibit a structural and functional disruption of the axon initial segment (AIS), a subdomain of the axon that acts as the trigger-zone for action potential generation. Importantly, this disruption is independent of myelin loss. Although the mechanism responsible for AIS disruption remains unclear, we observed an attenuation of the AIS insult following treatment with a known scavenger of oxygen free radicals. To further investigate the role of oxidative stress in modulating AIS stability, we employed an in vitro model in which neurons were exposed to a spontaneous reactive oxygen and nitrogen species generator. Through this approach, we demonstrated that oxidative stress is capable of AIS modulation acting through induction of cytosolic calcium (Ca2+) influx from both extracellular and intracellular sources, resulting in calpain protease activation. Furthermore, because rises in intracellular Ca2+ are central to these and other mechanisms of AIS disruption, we next investigated the cisternal organelle (CO), an AIS-localized Ca2+-regulating structure. Although this organelle could prove to be central to AIS modulation, very little is known about the mechanisms regulating its stability. Through this line of investigation, we provide the first evidence of pathological alteration to the CO in a disease state. This disruption precedes loss of AIS protein clustering and axo-axonic GABAergic input in both EAE and MS postmortem tissue. Overall, these studies reveal a primary axonal insult, independent of myelin loss, in a disease classically characterized as a white-matter pathology. Instead, this insult is most likely driven by oxidative stress through local Ca2+ dysregulation at the AIS, providing novel therapeutic targets for MS.