Multiple Sclerosis (MS) is a life-long chronic autoimmune disease diagnosed primarily in young adults who have a virtually normal life expectancy. Estimates place the annual costs of MS in the United States in excess of $2.5 billion. There are approximately 250,000 to 400,000 persons in the United States with MS, and approximately 2.5 million persons worldwide suffer from MS. A variety of therapies are used to treat MS, but there is no single therapy that can be used to treat all patients. Furthermore, therapies that are currently approved for MS are only moderately effective, and in some patients they have no effect at all. The invention provides a method to determine if a patient with MS will respond to a therapeutic protocol by analyzing the expression of genes expressed by the immune system. For example, a single gene can be assessed, or an expression profile of a patient can be created using an array comprising gene sequences and analyzed to determine if the patient will respond to one or more therapeutic protocols. A cDNA probe constructed from mRNA of lymphocytes isolated from a patient can hybridize with a microarray, and the extent of hybridization of the probes to each gene on the microarray can be determined. The microarray can include nucleic acid sequences encoding, for example, IL-8, Bcl-2-interacting protein, dihydrofolate reductase, gyanylate-binding protein 1, interferon-induced 17 kDa protein, 2’5’ OAS, plakoglobin, interferon inducible proteinkinase, and STAT-1, among others.