Brain and spinal cord atrophy occur early in the course of multiple sclerosis (MS) and continue throughout this lifelong illness, resulting in substantial parenchymal tissue loss at later disease stages. Treatments that slow or prevent atrophy may reduce disability progression in the long term. Disease-modifying agents (DMAs) such as interferon beta-1b (IFNbeta-1b), IFNbeta-1a, and glatiramer acetate inhibit inflammatory events believed to initiate and perpetuate the disease process. DMAs have been shown to inhibit aspects of MS related to brain inflammation such as relapses and gadolinium-enhanced lesions. Because brain inflammation has been linked to irreversible brain tissue injury, DMAs should be effective in reducing the rate of brain atrophy progression. Weekly IFNbeta-1a (Avonex or Rebif) has been shown to slow the rate of brain atrophy; a large study of a frequent injection regimen with IFNbeta-1a (Rebif) showed continued atrophy progression despite IFNbeta-1a at a rate similar to placebo-treated patients. It is not clear why weekly treatment regimens with lower total doses of IFNbeta-1a would show beneficial effects on brain atrophy compared with frequent injections with larger weekly doses. This article reviews results of clinical trials that have examined the effects of DMAs on brain and spinal cord atrophy in patients with MS. Some of these agents have demonstrated positive effects in well-controlled studies, suggesting that anti-inflammatory therapy can delay or prevent the emergence of irreversible central nervous system pathology.