Histopathology has demonstrated extensive grey matter (GM) damage in MS, and an association with meningeal inflammatory factors has previously been suggested. We applied a method to subdivide the cerebellar GM (CGM) into inner and outer regions, and investigated for magnetization transfer ratio (CGM-MTR) abnormalities in MS subtypes compared to healthy controls (HC). Outer was lower than inner CGM-MTR in all groups including HC. Outer and inner CGM-MTR reductions were observed in progressive MS subtypes. Stronger correlations of outer than inner CGM-MTR with clinical scores were observed, suggesting that outer CGM-MTR may reflect more clinically relevant pathology, particularly in progressive MS.