Magnetization transfer imaging (MTI) is a magnetic resonance imaging (MRI) technique that is now used in multiple sclerosis (MS) studies, and is thought to have a higher pathological specificity than conventional T2-weighted imaging. This review outlines the major contributions given by MTI for the understanding of MS evolution.MTI studies of individual MS lesions confirm the pathological heterogeneity of T2-weighted MRI abnormalities and the potential role of unenhanced T1-weighted hypointensities as specific markers of localized severe white matter disruption. Correlative cross-sectional and longitudinal studies using MIT and gadolinium (Gd)-enhanced MRI reveal that MTI findings may vary in lesions with different patterns of enhancement, and that MTI abnormalities are closely related to the onset and recovery of blood-brain barrier disruption in new MS plaques. MTI lesion load (LL) is highly correlated with T2-weighted MRI lesion load, but it has a limited reliability as a measure of MS lesion burden. On the other hand, measures obtained from MT scans using whole-brain histogram analysis are highly correlated with the extent of MS abnormalities on conventional MRI scans, and predict patients' clinical disability well, since they are sensitive to both macro- and microscopic MS lesion burden in the whole brain and in specific regions. These data suggest that (a) MTI is sensitive to different stages of lesion pathology and pathological evolution in MS patients; and (b) MT histogram analysis can provide a more global assessment of MS lesion burden, since it encompasses both macro- and microscopic MS pathology.