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The majority of clinical allogeneic haemopoietic cell transplants (alloHCT) are currently performed using reduced intensity conditioning (RIC) instead of myeloablative conditioning (MAC). However, most of the murine models for alloHCT and ensuing complications such as Graft versus Host Disease (GVHD) are studied with MAC models while the biology underlying RIC treatment remains incompletely understood.We investigated a new murine model of major histocompatibility complex (MHC)-matched multiple minor histocompatibility antigen mismatched alloHCT, using 10 x 106 bone marrow (BM) cells and 10-15 x 106 splenocytes from C57BL6 (H-2b) donor mice transplanted into BALB.B (H-2b) recipients after optimizing a RIC protocol consisting of 100mg/kg/day fludarabine for 5 days, 60mg/kg/day cyclophosphamide for 2 days, and sub-lethal total body irradiation (TBI). The MAC model consisted of cyclophosphamide 60mg/kg/day for 2 days and TBI of 850cGy. Mice were scored daily for severity of GVHD for 100 days post-transplant. In other groups of mice, tissue samples from RIC alloHCT mice were collected at different time points to assess the pathological and immunological features of GVHD compared to syngeneic RIC or allogeneic MAC transplant models.The lowest TBI dose capable of achieving complete donor chimerism with cyclophosphamide and fludarabine treatment in this strain combination was 325cGy. Mice given RIC had a reduced incidence and delayed onset of GVHD and significantly prolonged survival compared to MAC transplanted recipients. Similar to the MAC model, GVHD associated with RIC showed lymphocytic infiltration of portal tracts and damages bile ducts in liver. Gut pathology was less pronounced in RIC GVHD. In contrast, RIC mice with GVHD showed evidence of BM suppression, with anemia, reduced BM cellularity, and profound reduction in BM B cell lymphopoiesis, associated with damage to the endosteal BM niche. This was associated with an increase in BM CD8+ effector T cells in RIC mice, and elevated blood and BM plasma levels of Th1 cytokines. Increasing doses of splenocytes resulted in increased incidence of GVHD in RIC mice, which was dependent on donor CD8+ and CD4+ effector T cells. We have followed the upregulation of activation markers on donor and recipient dendritic cell and T cell populations in spleen and lymph nodes over time after RIC and MAC alloHCT to compare how the conditioning regimes contribute to immune activation.We demonstrate that the BM is a major target organ of GVHD driven by CD8+ and CD4+ effector T cells in an informative, clinically relevant, RIC alloHCT mouse model.