Multiple sclerosis (MS) has traditionally been considered to be primarily an inflammatory demyelinating disorder. Nowadays it is recognised as both an inflammatory and a neurodegenerative condition. This recognition is reflected in the development of new disease-modifying therapies that may offer the potential to reduce axon damage, either by inhibiting neurodegeneration or by promoting endogenous repair mechanisms. Since there is only a limited correlation between the clinical features of MS and findings on conventional magnetic resonance imaging (MRI), for the evaluation of such therapies new outcome measures are warranted. Grey matter atrophy occurs in the earliest stages of MS, progresses faster than in healthy individuals, and shows significant correlations with MRI lesion load, cognitive function and measures of physical disability; indeed, brain atrophy is the best predictor of subsequent disability and can be readily measured using MRI. Furthermore, it is becoming clear that currently available therapies differ in their effects on brain atrophy, and this may have important implications for the management of MS. New MRI techniques and advances in software development offer an opportunity to extend brain atrophy measurements beyond research studies to the routine management of MS patients.