PURPOSE OF REVIEW: To summarize recent evidence and current trends in the use of haematopoietic stem cell transplantation (HSCT) for autoimmune diseases. RECENT FINDINGS: Updates of published trials and data from the registries indicate a long-lasting, immunosuppression-free condition in about 50% of the patients who underwent an HSCT for a severe, progressive autoimmune disease. For all diseases, autologous HSCT is largely preferred for safety reasons, whereas allogeneic HSCT is to be considered only for carefully selected cases. Transplant-related mortality (TRM) has decreased in the past 5 years, due to both better selection of patients and the use of less intensive conditioning regimens. The most employed conditioning regimens in Europe are BCNU (carmustine), etoposide, ARA-C (cytosine arabinoside), M (melphalan) (BEAM)/anti-thymocyte globulin in multiple sclerosis and high-dose cyclophosphamide/anti-thymocyte globulin for all other diseases, with a trend for more intense regimens in North America. Multiple sclerosis and systemic sclerosis are currently the most frequent diagnoses. Prospective comparative trials are currently ongoing both in Europe and North America. SUMMARY: Recent reports confirm the evidence that HSCT is able to induce a high rate of sustained remissions in most severe autoimmune diseases, unresponsive to conventional treatments. Valuable information is expected by the finalization of the ongoing prospective, comparative trials.