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To investigate hypothalamic atrophy and its clinical correlates in multiple system atrophy (MSA) in-vivo. MSA is characterized by autonomic dysfunction and parkinsonian/cerebellar manifestations. The hypothalamus regulates autonomic and homeostatic functions and is also involved in memory and learning processes. 11 MSA, 18 Parkinson's Disease (PD) and 18 Healthy Controls (HC) were included in this study. A validated and automated hypothalamic segmentation tool was applied to 3D-T1-weighted images acquired on a 3T MRI scanner. MSA hypothalamic volumes were compared to those of PD and HC. Furthermore, the association between hypothalamic volumes and scores of autonomic, depressive, sleep and cognitive manifestations were investigated. Posterior hypothalamus volume was reduced in MSA compared to controls (t = 2.105, p = 0.041) and PD (t = 2.055, p = 0.046). Total hypothalamus showed a trend towards a reduction in MSA vs controls (t = 1.676, p = 0.101). Reduced posterior hypothalamus volume correlated with worse MoCA scores in the parkinsonian (MSA + PD) group and in each group separately, but not with autonomic, sleep, or depression scores. In-vivo structural hypothalamic involvement may be present in MSA. Reduced posterior hypothalamus volume, which includes the mammillary bodies and lateral hypothalamus, is associated with worse cognitive functioning. Larger studies on hypothalamic involvement in MSA and its clinical correlates are needed. • MSA is characterized by autonomic dysfunction and parkinsonian/cerebellar symptoms. • The hypothalamus role in MSA has been investigated pathologically, yet not in vivo. • We performed a structural MRI study investigating hypothalamic subregional volumes. • A reduction in posterior hypothalamus volume was found in MSA compared to PD and HC. • Posterior hypothalamus volume was associated with MoCA scores in MSA and PD. [ABSTRACT FROM AUTHOR]