Purpose: The immune modulatory effects of total lymphoid irradiation (TLI) for graft-versus-host disease (GVHD) protection and transplantation tolerance following allogeneic bone marrow and organ transplantation have been studied for years in animal models. In preclinical models non-myeloablative TLI conditioning alters residual host T cell subsets to favor regulatory natural killer (NK) T cells that suppress GVHD and prevent organ allograft rejection. These preclinical models have been recently adapted to human transplantation. Recent findings: Patients receiving allogeneic hematopoietic cell transplantation (HCT) for hematological malignancies conditioned with TLI and depletive T cell antibodies showed sustained donor chimerism, a reduced incidence of acute GVHD yet retained graft anti-tumor activity. As in the pre-clinical models, nonmyeloablative TLI conditioning significantly altered residual host T cell subsets favoring NK T cells, and the low incidence of GVHD was associated with increased IL-4 secretion by chimeric donor T cells. The TLI regimen used in cancer patients was modified to determine conditions for stable mixed chimerism and tolerance induction following combined hematopoietic cell and kidney transplantation. Summary: This review summarizes the evolution of the pre-clinical TLI protocols and their recent translation to clinical trials, and discusses the mechanisms involved in protection from GVHD and the induction of tolerance following mixed chimerism.