Mesenchymal Stem Cells (MSCs) represent a heterogeneous group of self-renewal, multipotent non-hematopoietic stem cells, which display profound immunomodulatory functions and promising therapeutic effects. Autoimmune diseases, which result from an aberrant immune response to selfantigens, can be detrimental to nearly all body tissues. With the advance in developing a novel treatment, including biological agents, it is still impossible to cure autoimmune disorders. Recent studies demonstrate the remarkable therapeutic effectiveness of MSCs towards a wide array of autoimmune diseases. In this review, the immunomodulatory influence of MSCs over immune cells and the application of MSCs transplantation in treating autoimmune diseases are highlighted.