Despite therapeutic advancements, graft versus host disease (GVHD) is a major complication of hematopoietic stem cell transplantation (HSCT). Pathogen and damage associated molecular patterns released following pre-transplant conditioning have an important role in the initiation of GVHD. However, the role of extracellular mitochondria (exMito) as an endogenous danger signal has not been explored. Herein, we report that cytotoxic conditioning with radiation leads to mitochondrial fission and impaired PINK-1/PARKIN-dependent mitophagy in the intestinal mucosal layer. This was coupled with extracellular release of damaged mitochondria in the plasma of BALB/c mice following irradiation. Sublethal irradiation of the Caco-2 epithelial cell line confirmed the in vivo expulsion of mitochondria in a cell-death independent manner. exMito released upon irradiation were damaged, and had impaired ATP production. Incubation of splenocytes with damaged exMito increased the cell surface expression of immune stimulatory molecules and induced Th1 cytokine release. Furthermore, in mixed lymphocyte reactions, exMito pre-treated BALB/c stimulator cells increased the activation and proliferation of C57BL6/J responder T cells. Finally, co-transplantation of isolated damaged mitochondria in a C57BL6/J to BALB/c mouse HSCT model aggravated GVHD. The translational relevance of these findings was studied in a cohort of pediatric patients who underwent HSCT. Fractionated irradiation given with their conditioning regimen increased the abundance of circulating exMito and correlated with the incidence of GVHD. Our results suggest that modulation of exMito release could be a novel therapeutic target to prevent GVHD after HSCT.