Autoimmune disease are complex disorders and therefore difficult to treat. In the past two decades, there has been a dramatic increase in our understanding of the pathophysiology of autoimmune diseases. A new era of treatments commenced. Instead of relying on non-specific immunosuppressive drugs alone, that were often a result of chance observations, it has become possible to design new therapeutic strategies on the basis of our new knowledge of autoimmune pathophysiology. New treatment regimens include manipulation of the immune system on the cellular and the humoral level as well as the cytokine level. Among the new treatment strategies, gene therapy is a particularly exciting approach for treating autoimmune diseases because it allows the delivery of therapeutic gene products in a site-specific manner, thus minimizing systemic side effects.