The successful application of post-transplantation cyclophosphamide (PTCy) as graft-versus-host disease (GVHD) prophylaxis in HLA-haploidentical allogeneic hematopoietic cell transplantation (allo-HCT) led to the expansion of its application to HLA-matched related and unrelated allo-HCT. Notably, single-agent PTCy was found to be feasible for GVHD prevention in HLA-matched bone marrow transplantation. Single-agent PTCy prophylaxis was later attempted to control GVHD in HLA-matched peripheral blood stem cell transplantation (PBSCT), but this approach was inadequate to alleviate GVHD as evidenced by the high incidence of severe GVHD and/or non-relapse mortality. Therefore, various combinations of immunosuppressants with PTCy have been explored to identify the optimal drug combination that would efficiently prevent GVHD in HLA-matched PBSCT. A recent murine study helped clarify the putative mechanism underlying the activity of PTCy, demonstrating that PTCy impairs the proliferation and function of alloreactive T cells from the donor, but does not eliminate alloreactive T cells altogether. In addition, imbalanced reconstitution of NK cell as well as T cells has been observed in HLA-haploidentical allo-HCT. Therefore, it remains unclear whether or not PTCy-containing GVHD prophylaxis should replace the classical GVHD prophylaxis regimen in the HLA-matched setting, and convincing evidence supporting the benefits of PTCy is needed.