Abstract: There are many categories of autoimmune diseases and the pathogenesis is still unknown. For those who are intolerant or poorly responsive to conventional therapies, other effective candidate treatment options need to be considered. Some therapies have shown great therapeutic prospects in the treatment of rheumatic diseases, including stem cell transplantation, biological agents, botanical drugs and some immunomodulatory substances. Their mechanisms of action and applications in autoimmune diseases were reviewed in this paper.