Nowadays the majority of multiple sclerosis (MS) research pays attention to the neurodegenerative component, using a magnetic resonance imaging voxel-based morphometry for its assessment. Cerebral atrophy occurs in the earliest stages of MS in different clinical phenotypes and progresses three times faster than in healthy individuals. WM atrophy involved almost all brain regions, but is less pronounced than GM loss. GM atrophy has distinct patterns of regional distribution in patients with different clinical phenotypes, more extensive in the progressive than in the relapsing disease phenotypes. Deep GM atrophy is demonstrated to correlate with WM lesion as well as cortical atrophy. GM atrophy shows significant correlations with T2 lesion volume, cognitive function and measures of physical disability. In addition to cerebral loss, MS patients frequently develop spinal cord atrophy, which also correlates with clinical impairment. However, the order of GM and WM involvement still remains unclear. And further research of atrophy MRI-predictors is needed in order to monitor clinical course of MS.