Autologous hematopoietic stem cell transplantation (AHSCT) has been proposed as a treatment modality which may arrest the autoimmune disease process and lead to sustained treatment-free remissions. Since the first consensus statement in 1997, approximately 200 autologous bone marrow or hematopoietic stem cell transplantations have been reported world-wide for SLE. The current state of AHSCT in SLE was reviewed at a recent meeting of the Autoimmune Working Party of the European Group for Blood and Marrow Transplantation. There was general agreement among experts in this field, that in patients with severe SLE refractory to conventional immunosuppressive therapies, AHSCT can achieve sustained clinical remissions (ranging from 50–70% disease free survival at 5 years) associated with qualitative immunological changes not seen with other forms of therapy. However, this clinical benefit is associated with an increase in short-term mortality in most but not all studies. Improving patient selection, long-term follow up of patients after AHSCT, optimization of induction and maintenance therapy along with detailed analysis of the immune system are identified as key areas for future research. Optimally, AHSCT should be compared to conventional therapy in randomized controlled trials. Development of stronger transplant registries, defining a core set of clinical data and standardizing biologic sample collections would make future collaborations and comparison of various studies more feasible.