Brain atrophy may occur early in the course of multiple sclerosis (MS) and may be associated with disability. Brain magnetic resonance imaging (MRI) of 114 MS patients (group A) were analyzed for regional atrophy (vs age-/gender-matched controls) and T1 and T2 lesions using 4-point rating systems. Thirty-five separate patients (group B) were analyzed for cortical atrophy (ordinal scale), third ventricular width, and total T2 hyperintense lesion volume (computer assisted). In group A, regression modeling indicated that inferior frontal atrophy (P = .0003) and T2 lesions in the pons (P = .02) predicted physical disability (Expanded Disability Status Scale [EDSS] score). Secondary progressive (SP) versus relapsing patients were predicted by inferior parietal (P = .002), superior parietal (P = .006), temporal (P = .008), inferior frontal (P = .01), superior frontal (P = .01), cerebellum (P = .01), occipital (P = .01), and midbrain (P = .02) atrophy. SP patients were also predicted by total atrophy (P = .01) and third ventricular enlargement (P = .03) but not T1 or T2 lesions. In group B, the regression model predicting EDSS score included only superior frontal atrophy (r = 0.515, P = .002). Mean kappa coefficients of ordinal ratings were 0.9 (intraobserver) and 0.8 (interobserver). Ordinal ratings correlated well with quantitative assessments. The authors conclude that brain atrophy is closely associated with physical disability and clinical course in MS patients and can be appreciated using a semiquantitative MRI regional rating system.