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However, little is known about the natural history of the disease. This motivated us to determine the extension and progression of central nervous system involvement in SCA3\/MJD using multimodal magnetic resonance imaging (MRI)\u2010based analyses in a large cohort of patients (n\u2009=\u200979) and presymptomatic subjects (n\u2009=\u200912).<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>All subjects underwent MRI in a 3T device to assess gray and white matter. To evaluate the cerebral and cerebellar cortices, we used measures from FreeSurfer and SUIT. T1\u2010multiatlas assessed deep gray matter. Diffusion tensor imaging multiatlas was used to investigate cerebral white matter (WM) and SpineSeg to assess the cervical spinal cord.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>There was widespread WM and cerebellar damage, in contrast to the restricted motor cortex involvement when all patients are compared to age\u2010 and sex\u2010matched controls. Presymtomatic patients showed WM microstructural abnormalities mainly in the cerebellar and cerebral peduncles and volumetric reduction of midbrain, spinal cord, and substantia nigra. To assess the disease progression, we divided patients into four subgroups defined by time from ataxia onset. There was a clear pattern of evolving structural compromise, starting in infratentorial structures and progressing up to the cerebral cortex.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Structural damage in SCA3\/MJD begins in the spinal cord, cerebellar peduncles, as well as substantia nigra and progresses to cerebral areas in the long term. These structural differences reveal some insights into the pathogenesis of SCA3\/MJD and suggest a staging scheme to map the progression of the disease. 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