Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is the only effective treatment for certain blood cancers and disorders. This is a life-saving, but dangerous procedure, with a high occurrence of side effects including infection and graft-versus-host-disease (GVHD). Numerous individual patient factors determine patient response to allo-HSCT, including intestinal microbiome composition. The intestinal microbiome is expected to influence immune system activity after allo-HSCT, but these details are yet unclear. We hypothesize that a personalized mixture of host, transplant, and microbial factors underpin the currently unpredictable risk of GVHD and infection following allo-HSCT.