Graft-versus-Host Disease (GVHD), is the most frequent and severe complication of allogeneic hematopoietic stem cell transplantation (HSCT). Much of our knowledge on the pathophysiology of GVHD has been gained from experimental models but far less from the study of the disease in humans. Recent developments in basic biology open new avenues to the development of biomarker sets that could predict GVHD severity and prognosis that could be tested and validated through well-designed multicenter clinical trials.