There are presently many magnetic resonance (MR) measures that can aid the assessment of damage to the brain. The conventional measures include T2 lesion volume, T1 enhanced lesion volume, and brain atrophy. Newer methodologies include magnetization transfer measures and proton spectroscopy. These methods have the potential for improving the specificity of MR with respect to the underlying pathology. MR spectroscopy offers the ability to quantitate the component of axonal loss in multiple sclerosis. MR techniques can be implemented to assess the effectiveness of treatment algorithms.