Autoimmune diseases are a group of chronic inflammatory conditions diseases characterized by aberrant activation of the immune system involving either cells or antibodies directed against normal tissues. The current conventional strategies, notably corticosteroids and immunosuppressors, are responsible for high treatment-related morbidity and are still associated with significant disease and treatment-related mortality. Recently, experimental and clinical data has suggested that mesenchymal stem cell transplantation would be a promising therapy strategy for the treatment of autoimmune diseases. This article will review the rationale and Chinese experience of mesenchymal stem cell transplantation in treatment of autoimmune diseases.