This review summarizes recent results investigating the role of certain cytokine gene polymorphisms, including those of TNF-alpha, IFN-gamma, IL-6, IL-10 and IL-1 receptor antagonist (IL-1Ra), in allogeneic stem cell transplantation. It discusses their role in predicting outcome and the development of a genetic risk index for graft versus host disease (GvHD) in HLA-matched sibling transplants. By the comparative use of an in vitro human skin explant model, initial results suggest that certain cytokine gene polymorphisms may be associated with more severe disease.