Immunosuppressive or immunomodulatory treatments are often used in patients with various autoimmune diseases (AID). However, since conventional treatments are rarely curative, alternative treatment methods have been looked for. Based on animal experiments and anecdotal case reports, stem cell transplantation (SCT) has received considerable attention in the treatment of severe autoimmune diseases during the last decade. This review summarizes current experience of SCT in patients this field. Although early experience shows some promise, randomized studies are necessary to evaluate the real value of autologous SCT in various autoimmune diseases. Since autologous SCT may not be curative in patients with AID, also evaluation of allogeneic SCT is important in the future.