Disclosed are improved methods for the treatment or prevention of an autoimmune disease comprising administration of a modified self-vector encoding and capable of expressing a self-polypeptide that includes one or more pathogenic epitopes associated with the autoimmune disease. The improved method of the present invention includes the administration to a subject of a modified self-vector or self-vectors comprising a polynucleotide encoding a self-polypeptide. In one aspect, the method includes a modified self-vector that allows for increased expression of the self-polypeptide associated with an autoimmune disease in a host cell relative to the unmodified vector. In another, non-mutually exclusive aspect, the method includes a modified self-vector that allows for a secreted autoantigen associated with an autoimmune disease to be encoded as a non-secreted self-polypeptide.