A ready-to-use guide for establishing and interrogating human and animal models of autoimmune diseases. Patr I contains methods and protocols to assess immunological and biochemical pathways relevant for disease pathogenesis. Part II contains protocols to establish and assess inflammatory arthritis, SLE, myocarditis, thyroiditis, experimental allergic encephalomyelitis (EAE, IDDM, scleroderma, uveitis, and vitiligo. All methods focus on assessment of genetic, immunological, and biochemical parameters underlying spontaneous or exogenous antigen-induced diseases.