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Haploidentical donor stem cell transplantation (haplo-SCT) has made great advances in recent decades. The granulocyte colony-stimulating factor (G-CSF)- and antithymocyte globulin (ATG)-based protocol, which is known as the Beijing Protocol, represents one of the current T-cell repletion strategies in haplo-SCT. The key elements of the Beijing Protocol for graft versus host disease (GvHD) prophylaxis include G-CSF inducing T-cell tolerance and altering graft cell components, as well as ATG administration exerting an immunoregulatory effect for intensive prophylaxis. This review will summarize the GvHD incidence, the underlying novel mechanism for GvHD prophylaxis, how to optimize GvHD prophylaxis, and the recent advances of the Beijing Protocol, mainly focusing on the issues of GvHD.