Autoimmune diseases are a severe human disorders. With the development of gene transfer technology, the study of gene therapy in autoimmune diseases has made some progress. By selecting the appropriate vector to transduce the immune regulatory molecules, defective gene, activating factor, apoptosis receptor into the body and induce the immune tolerance, etc. to achieve therapeutic purposes. Compared with the traditional treatment, gene therapy is more effective and targeted with little side effect. In this paper, the achievements of gene therapy for autoimmune diseases in pre-clinical and clinical trials in recent years were reviewed.