The purpose of this study is to evaluate the safety and efficacy of allogeneic bone marrow derived mesenchymal stem cell (AlloMSC) transplantation in patients with refractory SLE. Patients with Lupus nephritis and refractory to corticosteroid or cyclophosphamide trials will be enrolled in this trial. The treatment intervention includes a 24 hour pretreatment with cyclophosphamide followed by AlloMSC transplantation. Patients will be admitted to the in-patient service for the 3-5 days for the transplant treatment and will be followed up in the outpatient clinic. All baseline lupus serology, renal function panels will be obtained at pre-treatment admission. Post-transplantation follow-up visits will be at monthly intervals for lupus serology and renal function tests, and every 3 months for analysis of T regulatory population. The transplanted patients will be evaluated by an integrated team of rheumatologists, hematologists and bone marrow transplant specialists every month for the entire duration of the trial (2 years) and every 6-12 months thereafter.