Transcription factors of the Rel/NF‐κB family are known to play different roles in immunity and inflammation, although the putative role of c‐Rel in transplant tolerance and graft‐versus‐host disease (GVHD) remains elusive. We report here that T cells deficient for c‐Rel have a dramatically reduced ability to cause acute GVHD after allogeneic bone marrow transplantation using major and minor histocompatibility mismatched murine models. In the study to understand the underlying mechanisms, we found that c‐Rel^−/− T cells had a reduced ability to expand in lymphoid organs and to infiltrate in GVHD target organs in allogeneic recipients. c‐Rel^−/− T cells were defective in the differentiation into Th1 cells after encountering alloantigens, but were enhanced in the differentiation toward Foxp3⁺ regulatory T (Treg) cells. Furthermore, c‐Rel^−/− T cells had largely preserved activity to mediate graft‐versus‐leukemia response. Taken together, our findings indicate that c‐Rel plays an essential role in T cells in the induction of acute GVHD, and suggest that c‐Rel can be a potential target for therapeutic intervention in allogeneic hematopoietic cell transplantation in the clinic.