The disease progression in a mouse model of multiple sclerosis (EAE) was monitored based on regionally resolved brain viscoelasticity. Multifrequency MR elastography was applied prior to immunization and during subsequent phases of disease progression. Our results suggest that mechanical structures of the brain, particularly throughout the whole brain, in the cortex, and in the periventricular and hippocampal areas, are already significantly affected by neuroinflammation bevor clinical disability is manifested. Moreover, stiffness of the hippocampus and periventricular tissue transiently recovered during remission and became re-affected during relapse. This suggests that mechanical alterations are transient and recover during remission.