Magnetic resonance imaging is highly sensitive in revealing CNS abnormalities associated with several neurological conditions, but lacks specificity for their pathological substrates. In addition, MRI does not allow evaluation of the presence and extent of damage in regions that appear normal on conventional MRI sequences and that postmortem studies have shown to be affected by pathology. Quantitative MR-based techniques with increased pathological specificity to the heterogeneous substrates of CNS pathology have the potential to overcome such limitations. Among these techniques, one of the most extensively used for the assessment of CNS disorders is magnetization transfer MRI (MT-MRI). The application of this technique for the assessment of damage in macroscopic lesions, in normal-appearing white and gray matter, and in the spinal cord and optic nerve of patients with several neurological conditions is providing important in vivo information-dramatically improving our understanding of the factors associated with the appearance of clinical symptoms and the accumulation of irreversible disability. MT-MRI also has the potential to contribute to the diagnostic evaluation of several neurological conditions and to improve our ability to monitor treatment efficacy in experimental trials.