Autoimmunity after stem-cell transplantation has been observed over decades. Evidence comes from single case reports or small series. Autoimmune phenomena are known in both the autologous and the allogeneic settings, irrespective of the graft source. Most publications deal with autoantibody production after transplantation; more rarely, the appearance of the associated autoimmune disease is reported. Autoimmune thyroid disease and autoimmune cytopenias are most often described. Homeostatic expansion after transplantation-induced lymphopenia is thought to be a trigger for loss of self-tolerance and proliferation of autoreactive T-cells in these patients. With allogeneic haematopoietic stem-cell transplantation, adoptive transfer of autoimmune disease has been shown, raising the issue of graft quality. Many of the clinical and laboratory features of graft-versus-host disease (GvHD), especially in its chronic form, resemble those of autoimmune diseases, and the pathophysiological mechanisms are similar. Prospective data for a better understanding of autoimmunity and 'altered' immunity after stem-cell transplantation are needed.