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Use of high-dose, post-transplant cyclophosphamide (PTCy) results in low rates of graft-versus-host-disease (GVHD) and favorable immune reconstitution, although with higher rates of relapse and somewhat high rates of graft failure. We hypothesized that permissible dose reduction of PTCy might be feasible. The current study attempts to establish a murine model and focus on regulatory T cells (Tregs) to clarify the immunological mechanisms for GVHD prevention by low-dose PTCy. In addition, a prospective, clinical cohort study in haploidentical, T-cell replete transplantation is initiated to support the rational. We found that acute GVHD could be alleviated by low-dose PTCy and could be further mitigated after the combined use of low-dose PTCy and antithymocyte globulin (ATG) in mice. Flow-cytometric analyses in mice showed that low-dose PTCy could increase the number of Tregs and the effect on Tregs is significantly prominent with the combined use of low-dose PTCy and ATG. In the clinical cohort study, the cumulative incidence of grades II-IV acute GVHD in combined treatment cohort with low-dose PTCy and ATG/granulocyte colony-stimulating factor (G-CSF) (17%; 95% CI, 5–29%) was significantly lower than both that in matched-pair cohort (33%; 95% CI, 25–41%; P = 0.04) and that in historical cohort (56%; 95% CI, 42–70%; P < 0.001). In-vivo immune reconstitution analysis showed that low-dose PTCy could facilitate suppressive Tregs reconstitution. In conclusion, low-dose PTCy is sufficient for GVHD abrogation under lymphopenic situation and can enhance the protective effect of ATG/G-CSF on GVHD. Intensified conditioning followed by low-dose PTCy might be a feasible option for patients undergoing haploidentical transplantation. [ABSTRACT FROM AUTHOR]