Studies have shown that experimental allergic encephalomyelitis, a model for Multiple Sclerosis, can be inhibited by repeated administration of anti-inflammatory cytokines or cytokine neutralising agents. Given the short half-life of many biological agents, administration must be frequent to maintain a therapeutic effect. Gene therapy allows long-term in vivo delivery of these biological therapeutic agents. This study has investigated the use of viral and non-viral vectors administered systemically and locally to the central nervous system, to deliver the anti-inflammatory cytokines IL-4, IL-10 TGF-β and IFN-γ with the aim of ameliorating EAE. In addition, neutralisation of TNF using soluble TNF receptors and blockade of T-cell costimulation using CTLA4-Ig fusion proteins and anti-B7 antibodies were also studied. This study demonstrates that EAE can be successfully inhibited using gene delivered biological agents by a variety of vectors, either during the priming stage of disease or after disease onset. Local administration of the vector to the CNS increases the efficacy of therapeutic agents even at lower doses than used systemically, and may reduce the systemic side effects seen with standard high-dose protein therapy. The study of currently available vectors under the same conditions and in the same model allows a useful comparison and highlights both advantages and disadvantages of each method. This study provides data on a variety of successful approaches of gene delivery to treat an ongoing CNS autoimmune disease, which hopefully will provide a basis for using this method in humans.