The degree of disability and cerebellar and brainstem impairments in multiple sclerosis (MS) patients were correlated with several magnetic resonance imaging (MRI) measures of tissue damage in the whole brain, cerebellum and brainstem to determine the relative contributions of the factors underlying the development of disability in MS. Dual-echo conventional spin-echo, T(1)-weighted and magnetization transfer (MT) scans were obtained from 72 patients with MS and 20 age- and sex-matched controls. The following MRI-derived quantities were considered for the brain as a whole, for the cerebellum and for the brainstem: (a) the number and volume of lesions seen on T(2)-weighted images; (b) the number and volume of lesions seen on T(1)-weighted images; (c) the size of these structures measured on T(1)-weighted scans; (d) the average MT ratio (MTR), peak height and peak position for the MT histogram. With univariate analysis, many MRI measures were significantly different in patients with different levels of disability or cerebellar and brainstem functional system impairments. However, with multivariate analysis, only whole-brain average MTR was significantly related to physical disability, while cerebellar and brainstem T(1) lesion volume and average MTR were related to cerebellar and brainstem impairment. This study shows that increased pathological damage in clinically eloquent sites is the major cause of disability in patients with MS. It also suggests that measures derived from MT histogram analysis and T(1) hypointense lesion load should be considered when evaluating long-term MS evolution.