This study attempts to evaluate the outcome of autologous peripheral blood hematopoietic stem cell transplantation (auto-PBHSCT) in patients with severe paediatric systemic lupus erythematosus (SLE). Five patients (n = 2 females, n = 3 males) with severe or refractory paediatric SLE received autologous peripheral blood CD34+ cell transplants between July 2005 and February 2009. The patients ranged in age from 6 to 14 years, and the course of disease extended over a period from 5 to 90 months. All of the patients received conventional therapy for 3 to 87 months. After their discharge from the hospital, the patients continued to maintain their regular follow-up visits and basic quality of life. The patients exhibited decreased immune function after the auto-PBHSCT. The CD4+ and CD19+ cells were significantly reduced. Viremia occurred in four patients 2 months after the transplantation. All of the patients went into clinical remission in 3-6 months. The severity of encephalopathy, nephritis and organ damage declined in varying degrees. The disease recurred in patient 2 at 9 months and in patient 4 at 12 months after the transplantation. Because the disease was relatively mild, we were able to administer small doses of glucocorticoids that were sufficient to control the course of the disease. Macrophage activation syndrome occurred in patient 3 at 18 months after the transplantation. At the end of the follow-up period, three of the five patients were completely off their medications. Another two patients sustained small doses of glucocorticoids. The developmental levels of these patients were comparable to those of normal children at the end of the follow-up. The quality of life improved significantly. The auto-PBHSCT is effective for severe and refractory paediatric SLE. The incidence of lethal infection and other adverse reactions is low. Long-term remission can be achieved. A milder form of the disease may have recurred after the transplantation.