A new model of multi-compartment auto-immune disease has been established to analyze the effects of polyvalent recombinant peptide vaccines. A synthetic gene encoding major pathogenic determinants for Lewis rats of guinea pig myelin basic protein (MBP68-84), bovine interphotoreceptor retinoid binding protein (IRBP1169-1191), and bovine P2 protein (P2,53-78) was used to induce Generalized Autoimmunity of the Nervous System (GANS), which is characterized by development of auto-immune infiltration of the brain and spinal cord, the eyes, the pineal organ and the peripheral nerves. Thus, this model integrates the prominent features of three auto-immune diseases: experimental autoimmune encephalomyelitis (EAE), neuritis (EAN) and uveitis (EAU). In this study, GANS was used to study the effect of HIV-1 Tat37-72 targeting peptide on vaccination by recombinant polyvalent T cell auto-antigen vaccine. Depending on the route of administration, the recombinant vaccine effectively protects against the development of auto-immune nervous system inflammation.