Grey matter atrophy has become a clinically relevant marker of progressive disability in multiple sclerosis (MS). To better study atrophy in MS, mouse models that have grey matter loss are needed. A possible candidate is the experimental autoimmune encephalomyelitis (EAE) mouse model. We used high-resolution magnetic resonance imaging (MRI) and atlas-based regional volumetrics to measure the volumes of 62 structures in the brains of EAE mice, 66 days post-induction. We identified atrophy in 19 structures including the cortex, cerebellum, striatum, thalamus, hippocampus, and corpus callosum. Using MRI we can study atrophy in this inflammatory model of MS.