The hypothesis that haematopoietic stem cell transplantation (HSCT) might be useful in treating refractory autoimmune diseases (AID) was suggested by studies in animal models and by the improvement of concurrent autoimmune diseases in patients who had undergone transplantation for haematological disorders. This concept has now been tested in a substantial number of phase I/II clinical trials of autologous HSCT. These early results are promising, even in patients who have failed on multiple standard therapies for AID. Transplantation-related toxicity has decreased with growing experience in the application of this procedure, better patient selection and the modification of treatment protocols. Randomized trials currently under way or under consideration should clarify the role of HSCT in patients with autoimmune disorders.