The efficacy of allogeneic hematopoietic stem cell transplantation (allo-HSCT) is currently limited due to the occurrence of acute and chronic graft-versus-host disease (GVHD). Obesity is pandemic but its impact on HSCT outcomes is poorly understood. We report here that obesity has a negative and selective impact on acute GVHD. Diet-induced obese (DIO) mice exhibited increased gut permeability, endotoxin translocation and radiation-induced gastrointestinal damage. After allo-HSCT, DIO recipients across strains and sex had markedly increased pro-inflammatory cytokines (IL-6, TNF, ST2), MHC class II expression and exhibited rapid mortality associated with severe acute gut pathology. This rapid and acute obesity-associated gut GVHD was totally dependent on donor CD4 T cells and occurred even in minor MHC mismatch strain combinations where lean recipients presented only with much delayed chronic skin GVHD. Combined pro-inflammatory cytokine blockade targeting both IL-6 and TNF could protect DIO recipients without compromising concurrent graft-versus-tumor (GVT) effects. Retrospective analysis of a clinical cohort using unrelated HLA haploidentical HSCT recipients revealed that recipients with a high body mass index (BMI>30) had significantly reduced survival and higher serum ST2 levels compared to non-obese recipients mirroring the preclinical outcomes. Assessment of both DIO mice and high BMI HSCT patients also revealed markedly reduced microbiome diversity and decreased Clostridiaceae abundance. Extended prophylactic antibiotic treatment of DIO mice protected from the endotoxin translocation, cytokine storm as well as gut GVHD pathology but did not protect later development of chronic skin GVHD. These results demonstrate in both mice and humans that obesity alters the microbiome and imparts differential effects on GVHD following allo-HSCT with decreased survival in both; in mice this inferior outcome can be pre-empted by combined pro-inflammatory cytokine blockade or antibiotic pretreatment.