Systemic lupus erythematosus (SLE) is a complex autoimmune disease with multiorgan involvement and high mortality, which was reduced because of the most widely and classically used immunosuppressive therapies. However, some patients continue to have significant mortality. So a shift in the approach to the treatment of SLE is needed. In the past decade, most transplants have been performed in the treatment of SLE with allogeneic or autologous hematopoietic stem cells and currently emerging mesenchymal stem cells. There are some important differences between the two procedures.