Graft-versus-host disease (GvHD) is a major cause of morbidity and mortality in patients treated with allogeneic hematopoietic stem cell transplantation (HSCT). Post-transplant immunosuppressive drugs incompletely control GvHD and increase susceptibility to opportunistic infections. In this study we used flagellin, a TLR5 agonist protein (~50 kDa) extracted from bacterial flagella, as a novel experimental treatment strategy to reduce both acute and chronic GvHD in allogeneic HSCT recipient. Based upon the radio-protective effects of flagellin, we hypothesized that flagellin could ameliorate GvHD in lethally irradiated murine models of allogeneic HSCT. Two doses of highly purified flagellin (administered 3 hrs. before irradiation and 24 hrs. after HSCT) reduced GvHD and led to better survival in both H-2b → CB6F1 and H-2k → B6 allogeneic HSCT models while preserving over 99% donor T cells chimerism. Flagellin treatment preserved long-term post-transplant immune reconstitution characterized by more donor thymic-derived CD4+CD25+foxp3+ regulatory T cells (Tregs) and significantly enhanced anti-viral immunity following murine cytomegalovirus (mCMV) infection model. The proliferation index and activation status of donor spleen-derived T cells, and serum concentration of pro-inflammatory cytokines in flagellin-treated recipients were reduced significantly within 4 days post-transplant compared with the PBS-treated control recipients. Allogeneic transplantation of radiation chimeras previously engrafted with TLR5 knockout hematopoietic cells showed that interactions between flagellin and TLR5 expressed on both donor hematopoietic and host non-hematopoietic cells were required to reduce GvHD. Thus, the peri-transplant administration of flagellin is a novel therapeutic approach control GvHD while preserving post-transplant donor immunity.