Many studies of autologous hematopoietic stem cell transplantation (HSCT) and allogeneic HSCT have been conducted for autoimmune disease in various animal models. Because of the substantial risk of morbidity and mortality associated with allogeneic bone marrow transplantation, autologous transplants justified trying this approach in patient with severe autoimmune disease who were refractory to current treatments. Remission was achieved in some of the patients and some of them relapsed. Recently, many in vitro studies have reported that mesenchymal stem cells (MSC) have immunomodulatory properties and immunosuppressive effects on MHC-mismatched lymphocytes proliferation by inhibiting naïve, memory and activated T cells, B cell, NK cells and dendritic cells. In addition, adipose tissue-derived MSC (AT-MSC) are becoming an alternative source of MSC for therapeutic applications because adipose tissues are abundant, easily accessible, easily obtainable with little patient discomfort and large amounts of AT-MSC can be easily obtained. A large body of in vitro research has shown that AT-MSC have same or similar immunomodulatory effects with bone marrow derived MSC. Drawing on this finding, the increasing numbers of researchers have turned on their attention to preclinical studies on AT-MSC. As this new path of research evolves with subsequent reports, MSC would make a significant contribution to stem cell therapy or combination therapy for ameliorating symptoms and curing autoimmune disease. By searching and studying the appropriate therapeutic gene, the therapeutic gene transfected stem cell therapy will be able to acquire the synergy effect and the combined advantage of gene therapy and stem cell therapy.