OBJECTIVE: Spinocerebellar ataxia (SCA) is a neurodegenerative disorder in which, autonomic dysfunction is a common manifestation. Brain area atrophy also involves the areas comprising central autonomic network (CAN) in SCA. Structural atrophy of CAN and autonomic dysfunction should go hand in hand. But this important relationship has not been studied to date. Therefore, using SCA as a disease model, the present study has been designed to explore the plausible correlations between the brain areas of CAN and clinical autonomic function modalities in SCA patients. MATERIALS AND METHODS: 3D T1-weighted scans were acquired on 3T MRI, analyzed by FreeSurfer software in genetically confirmed forty-nine SCA patients (SCA1 = 18, SCA2 = 25 and SCA3 = 6). Heart rate variability (HRV), blood pressure variability (BPV), baroreflex sensitivity (BRS), and autonomic reactivity tests were used for evaluation of autonomic nervous system. Additionally, autonomic dysfunction scoring was done using composite autonomic severity score (CASS). RESULTS: On correlation analysis, the study showed the association of atrophic cortical and subcortical brain areas (predominantly prefrontal cortex, bilateral middle temporal, left cuneus, left lingual and left caudate) with altered clinical autonomic function parameters in SCA patients. These areas were primarily comprised of sympathetic and parasympathetic brain areas of CAN. One of the key brain areas of CAN - left cuneus was found to be associated with both HRV (r = 0.295, p = 0.040) and BRS (r = 0.326, p = 0.022). CONCLUSION: A characteristic pattern of association between particular brain areas of CAN and clinical autonomic function parameters was observed in SCA patients.