Experimental autoimmune encephalitis (EAE), the animal model of multiple sclerosis (MS), has provided significant insight into the mechanisms that initiate and drive autoimmunity. Several central nervous system proteins and peptides have been used to induce disease, in a number of different mouse strains, to model the diverse clinical presentations of MS. In this chapter, we detail the materials and methods used to induce active and adoptive EAE. We focus on disease induction in the SJL/J, C57BL/6, and BALB/c mouse strains, using peptides derived from proteolipid protein, myelin basic protein, and myelin oligodendrocyte glycoprotein. We also include a protocol for the isolation of leukocytes from the spinal cord and brain for flow cytometric analysis.