The maximum tolerated dose of FOS was determined to be 10 g/day, with transient effects on the gut microbiome and possible immunomodulatory effects on Tregs, limited primarily by nausea and mucositis. No significant differences were found between the FOS and control groups in rates of acute GvHD, bloodstream infections, C. difficile infections, or overall mortality. Patients receiving FOS had higher peripheral blood concentrations of CTLA4+ CD4+ activated T cells (likely Tregs) at Day 28 post‐transplant compared to controls. This evidence concerns the gene CD4 and graft versus host disease.