We have recently demonstrated that CD3+CD4-CD8- double negative (DN) T cells can down-regulate allogeneic immune responses both in vitro and in vivo by killing activated syngeneic CD8+ T cells. The goal of this study was to identify molecules that are crucial for DN T cell-mediated suppression. We demonstrate that Ly-6A (Sca-1) is highly expressed on DN T cells. Incubation with IL-10 significantly reduced Ly-6A expression and the function of DN T cells. DN T cell-mediated killing was significantly reduced when Ly-6A was blocked.Ly-6A-deficient mice showed an accelerated allograft rejection when compared to wild-type controls. Furthermore we demonstrate that pretransplantation donor lymphocyte infusion (DLI) led to activation and proliferation of recipient DN T cells and prolongation of bm1-->B6 skin allograft survival. However, when the recipients were deficient in Ly-6A, the beneficial effect of DLI on allograft survival was abolished. Moreover, deficiency in Ly-6A did not affect the activation and proliferation of DN T cells. Rather, it impaired the ability of DN T cells to kill activated anti-donor CD8+ T cells. Taken together, our data indicate that Ly-6A plays a crucial role in DN T cell-mediated regulation in vitro and in vivo, perhaps by enhancing DN-CD8+ T cell signaling.