The contribution of natural CD4(+)CD25(+) regulatory T cells (nTregs) in controlling graft rejection and the mechanism used remain controversial. Using the duality of the 2.102 TCR Ag recognition, we were able to study, for the first time to our knowledge, the involvement of nTregs in the two pathways of allorecognition in a murine adoptive transfer model in which TCR-transgenic nTregs were or were not depleted before transplantation. We show that nTregs used at a physiological ratio were able to delay graft rejection after direct alloreactivity by controlling proliferation and differentiation of alloreactive CD4(+) conventional T cells in draining lymph nodes. In contrast, similar results were found in the indirect alloreactivity pathway only when nTregs were used in high numbers. In the latter pathway, nTregs used at a physiological ratio failed to delay graft rejection and to control proliferation of conventional T cells. These results support recent therapeutic approaches aimed at producing and using in vitro Ag-specific Foxp3(+) nTregs to control graft rejection in transplantation. Finally, late inhibition of Th1 differentiation was shown in indirect alloreactivity, but this suppression could also be mediated by Foxp3(+)-induced Tregs.