We used SPM99 to obtain normalized whole brain volumes of gray matter, white matter, and total parenchyma in patients with multiple sclerosis (MS) (n = 41) and age-/sex-matched normal controls (n = 18). As SPM99's automated gray/white matter volumes were significantly influenced by tissue compartment misclassification due to the effect of MS-related brain lesions, we corrected these automated volumes for misclassification before performing our primary analyses. For MS patients (disease duration = 9.5 ± 6.3 years; EDSS score = 3.2 ± 1.8; 25FTW = 6.6 ± 3.1 s), we also measured lesion load (total T1 hypointense [T1LV] and FLAIR hyperintense lesion volume [FLLV]), central brain atrophy (third ventricular width [TVW] and bicaudate ratio [BCR]), and clinical status (Expanded Disability Status Scale [EDSS] and 25-ft timed walk [25FTW]). Patients with MS had lower gray matter (707 ± 33 cm³ [−3.9%], P = 0.003) and total parenchymal volume (1088 ± 48 cm³ [−3.8%], P = 0.003), but only a trend for lower white matter volume (381 ± 25 cm³ [−3.7%], P = 0.052) relative to normal controls (gray matter: 736 ± 33 cm³; total parenchyma: 1132 ± 49 cm³; white matter: 396 ± 26 cm³). Gray matter atrophy was related to clinical status (EDSS, 25FTW, and disease duration), lesion load (T1LV and FLLV), and central brain atrophy (TVW and BCR), whereas white matter atrophy was related to only central brain atrophy. These findings suggest that gray matter loss is related to other aspects of brain pathology and has more clinical relevance than white matter atrophy in MS.