OBJECTIVE: To determine the safety and efficacy of immune ablation followed by autologous hematopoietic stem cell transplantation (HSCT) in refractory systemic lupus erythematosus (SLE). METHODS: Three patients who had been refractory to steroid and one or more immunosuppressive drug were included. Peripheral blood stem cells were mobilized with cyclophosphamide (CTX, 3 g/m(2)), followed by granulocyte-colony stimulating factor (5mug/kg/day). T lymphocytes were depleted from the graft by selection of CD34 positive cells. Conditioning regimens composed of high dose CTX (total dose 200 mg/kg) and anti-thymocyte globulin (total dose 90 mg/kg) in 2 patients and BEAM (BCNU 300 mg/m(2), etoposide 200 mg/m(2), cytarabine 200 mg/m(2), melphalan 200 mg/m(2)) in 1 patient. Stored stem cells were reinfused 48 hours after conditioning. RESULTS: Among 3 patients, first patient had lupus nephritis, second patient had overlap syndrome combined with rheumatoid arthritis (rhupus) and the last patient had severe thromobocytopenia and intractable polyserositis. No life threatening complications were observed during the treatment. All patients demonstrated rapid and marked improvement in organ function and quality of life just after HSCT. Previous massive proteinuria in first patient was decreased to less than 500 mg/day with 6 months follow up. Rhupus patient satisfied American college of rheumatology 70% response criteria with 3 months follow up. But third patient improved polyserositis dramatically 1 month after HSCT and relapsed at 9 weeks. CONCLUSION: In refractory SLE patients, HSCT can be performed safely with marked improvement and sustained withdrawal of all immunosuppressive medication. A further randomized trial is needed to confirm the efficacy and durability of remission.