To determine the role of allogeneic, autologous and syngeneic hemopoietic stem cell transplantation (SCTx) as a treatment for severe autoimmune disease (AID) we performed a literature search employing Medline, Cancer Lit and abstract books for reports on transplants for blood disorders and a concomitant AID. All reviews, case reports and abstracts available between June 1977 and September 2001 were used and attempts made to update them by e-mail by the corresponding authors. Disease-free survival (DFS) after allogeneic SCTx for 23 patients with severe aplastic anemia was 78% at 16 years and survival in unmaintained remission of concomitant AID was 64% at 13 years. DFS after allogeneic SCTx for 24 patients with hematologic malignancies was 87% at 15 years and survival in unmaintained remission for concomitant AID was 70% at 11 years. DFS after autologous SCTx for 24 patients with hematologic malignancies was 48% at 6 years and survival in unmaintained remission for concomitant AID was 29% at 3 years. Among 30 patients given allogeneic SCTx 19 developed graft-versus-host disease (GVHD) and 11 did not. Upon clinically justified discontinuation of all immunosuppressive therapy, 3/11 patients without GVHD relapsed with their concomitant AID (freedom of AID-relapse 69% at 9 years), whereas none of 19 patients with GVHD did so (log rank: P = 0.0135). Freedom of AID-relapse was superior after allo SCTx compared to autologous SCTx (89% at 18 years vs 38% at 5 years; log rank: P = 0.0002). Our data suggest that a graft-versus-autoimmunity effect after allogeneic hemopoietic SCTx mediates elimination of autoimmunity.