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The prognosis of patients with autoimmune diseases has improved dramatically over the last few decades. Aggressive immunosuppressive therapy is effective in the acute management of many of the most severe major organ manifestations. Other interventions, such as the use of angiotensin-converting enzyme inhibitors in scleroderma renal crisis and better management of various comorbidities, have contributed significantly to the improved outcomes. The emergence of immuno-modulatory biologic agents opened up a new field of targeted therapies, with remarkable successes in some diseases. These advances changed the nature of the most severe" forms of systemic autoimmune diseases from rapidly progressing, often fatal conditions to chronic diseases with variable but slower rates of progression. However, none of the currently used treatments is universally effective or has the potential to cure autoimmune diseases. Therefore, we have to continue to explore new approaches not only to improve the long-term outcome in patients with the most severe manifestations, but also to try to find a possible cure for autoimmune diseases. Hematopoietic stem cell transplantation (HSCT) has been considered a way to achieve both of these goals.