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Objective: To quantify spinal cord atrophy and its impact on clinical disability in spinocerebellar ataxia (SCA) type 3 and 6., Methods: Atrophy of the upper spinal cord was assessed by high resolution T1-weighted MRI of patients with SCA3 (n = 14) and SCA6 (n = 10). Furthermore, two groups of age- and sex-matched healthy control subjects (n = 24,) corresponding to the two SCA groups, were studied. Images were post-processed by a semi-automated volumetry method combining a marker based segmentation and an automatic histogram method facilitating highly reliable quantification and morphometry of the upper cervical cord in vivo., Results: We found a significant reduction of normalized mean crosssectional area of the spinal cord in SCA3 (p < 0.0005), whereas in SCA6 patients normalized mean crosssectional area was in the normal range (p = 0.379). No correlation was found between spinal cord atrophy and disease duration as well as CAG repeat length in both subtypes. In SCA6 a negative dependency between clinical disability, as expressed by the International Cooperative Ataxia Rating Scale as a well established ataxia score, and the mean cross-sectional area was found (p = 0.02). A similar correlation was observed in SCA3 but did not reach statistical significance., Conclusion: Our results quantify for the first time in vivo spinal cord atrophy as a non-cerebellar neurodegenerative process in SCA3. Our results suggest MR volumetry of the upper cervical cord as a marker of functional importance in SCA3 and SCA6.