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Transcranial magnetic stimulation (TMS) is a flexible, non-invasive technique that involves the production of a brief magnetic field to stimulate the conductive structures of the brain. When TMS is specifically employed as a single- or paired-pulse over the motor cortex, the function and integrity of the descending motor pathways can be assessed through the generation of a motor evoked potential (MEP). Important MEP-derived measures include the motor threshold, MEP amplitude and latency, central motor conduction time, silent period, intracortical inhibition, and intracortical facilitation. These functional measures may have use in individuals with multiple sclerosis (MS), a common chronic autoimmune disorder of the central nervous system, due to their useful diagnostic and prognostic implications. As a representation of excitability and conductivity, TMS measures may have the potential to serve as objective markers of corticospinal tract integrity, which is a major aspect of clinical disability in MS. Additionally, TMS may be employed to help monitor and provide insight on the effects of therapies for patients with MS over a longitudinal timeframe. In this review, we focus on the application of TMS in the context of MS, with an emphasis on the relationship between TMS measures and widely used clinical assessment measures used for patients with MS.