Multiple sclerosis (MS) and other autoimmune diseases result from the dysregulation of genetic and proteomic programs. In MS, the loss of immune homeostasis leads to aberrant targeting and destruction of the myelin sheath, which manifests as the clinical syndrome of MS. The advent of technologies to perform large-scale analysis of mRNA transcript and protein expression will transform our understanding of the mechanisms underlying the initiation and progression of MS, and will yield new targets for therapeutic intervention.