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Our previous data have revealed that proteinuria, antinuclear antibodies and anti-dsDNA antibodies in refractory systemic lupus erythematosus (SLE) reduced after MSC infusion. This study focused on the roles of mesenchymal SCT (MSCT) in SLE patients with refractory cytopenia. Thirty-five SLE patients with refractory cytopenia were enrolled in a MSCT trial. Hematological changes of pre- and post-transplantation were evaluated. Mechanisms for MSCT effects focused on the analysis of percentage of regulatory T cells (Treg) and Th17. The results showed that in 35 SLE patients, 20 patients had leukopenia, 24 with anemia or thrombocytopenia. The average follow-up period after MSCT was 21 months (range 6-45 months). Significant improvements in blood cell count were found after MSCT for most patients, in parallel with the decline of disease activity. Clinical remission was accompanied by increased Treg and decreased Th17. Two patients died of uncontrolled disease recurrence after infection, whereas no adverse events related to transplantation was observed. The result suggested that MSCT could reverse hematological aberration in SLE patients with refractory cytopenia, which might be associated with reconstitution of Treg and Th17. Longer follow-up and clinical larger-scale controlled study, as well as the exact mechanism exploration, will need further investigations.