The possible role of haematopoietic SCT (HSCT) for the treatment of severe autoimmune diseases was originally supported by animal experiments and remission of concomitant autoimmune diseases in patients undergoing transplantation for haematological disorders. Since 1996, over 100 procedures were performed in children with different severe autoimmune diseases such as juvenile idiopathic arthritis, systemic lupus erythematosus, systemic sclerosis, immune cytopaenias and Crohn's disease. This review tries to summarize the published data on efficacy and toxicity of HSCT in this group of patients.