Recurrent neuroinflammation in relapsing-remitting MS (RRMS) is thought to lead to neurodegeneration, resulting in progressive disability. Repeated magnetic resonance imaging (MRI) of the brain provides non-invasive measures of atrophy over time, a key marker of neurodegeneration. This study investigates regional neurodegeneration of the brain in early-stage RRMS using volumetry and voxel-based morphometry (VBM).RRMS patients (N=354) underwent 3T structural MRI at diagnosis and 1-year follow-up, as part of the Scottish multicentre ‘FutureMS’ study. MRI data were processed using FreeSurfer to derive volumetrics, and FSL for VBM (grey matter (GM) only), to establish patterns of change in GM and normal-appearing white matter (NAWM) over time throughout the cerebrum, cerebellum and brainstem.Volumetric analyses showed a decrease over time (q<0.05) in bilateral cortical GM and NAWM, multiple subcortical structures, cerebellar GM and the brainstem. Additionally, NAWM and GM volume decreased respectively in the following cortical regions, frontal: 14 out of 28 regions and 17/28; temporal: 18/18 and 15/18; parietal: 14/14 and 11/14; occipital: 7/8 and 8/8. Left GM and NAWM asymmetry was observed in the frontal lobe. GM VBM analysis showed three major clusters of decrease over time: 1) temporal lobe and subcortical areas, 2) cerebellum, 3) anterior cingulum and supplementary motor cortex; and four smaller clusters within the occipital lobe.Widespread neurodegeneration was observed in early-stage RRMS; particularly in the brainstem, cerebellar GM, and subcortical and occipital-temporal regions. Volumetric and VBM results emphasise different as well as overlapping patterns of longitudinal change, and provide potential response markers for existing therapies and trials of neuroprotective agents.