Magnetization transfer imaging (MTI) is a magnetic resonance imaging (MRT) 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 MTI 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 MTI 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.