Stem cells are a kind of multipotential differentiated cells with the ability of selfreplication. Under certain conditions, they can differentiate into multiple functional cells and replace the dead and nonregenerating cells to achieve the curative effects. Stem cell therapy is irreplaceable for nonregenerative cell injury. Currently, various stem cell products have been approved for the treatment of clinical diseases, such as osteoarthritis, myocardial infarction and diabetes. Autoimmune diseases have immune disorders, while stem cells can regulate immune. Advantages of stem cells for the treatment of autoimmune diseases, therefore, is not only that stem cells can differentiate regeneration for function cell, replace and repair the death and damaged cells, stem cells have the immune adjustment function, which can intervene and prevent the development of autoimmune diseases. The treatment effects and prospect of stem cells application in autoimmune diseases have more advantages than other diseases. Unfortunately, up to now, there are no stem cell products available worldwide for the treatment of autoimmune diseases. Based on the current available stem cell products and clinical studies on stem cells treatment in autoimmune diseases, We predict which stem cell products are most likely to be used for autoimmune diseases.