Acute graft-versus-host disease (aGVHD) remains a common life-threatening complication associated with allogeneic hematopoietic cell transplantation (allo-HCT) and is a major contributor to posttransplant mortality and morbidity. In allo-HCT, allogeneic T cells recognize host tissues as foreign and mount an immune response, causing inflammation and tissue damage. Traditionally, GVHD patients receive a regimen of immunosuppressive glucocorticoids after the onset of symptoms; however, many groups are developing prophylactic strategies due to the consequences associated with long-termLong-term effect glucocorticoid administration. Despite the advances made to mitigate GVHD, it remains a risk following allo-HCT; thus, new therapies are required to improve the safety of this therapy. Here, we use a prophylactic strategy that leverages graft manipulation as a way to induce tolerance upon transplantation. This chapter focuses on the techniques involved in conditioning donor cells, transplantation, and posttransplantation analysis of immune cells in a murine major histocompatibility complex (MHC) mismatched model of GVHD.