Allogeneic hematopoietic stem cell transplantation (SCT) remains the only available curative therapy for hematological malignancy. It does, however, result in significant morbidity and mortality, predominantly as a consequence of infections, leukemic relapse and graft-vs-host disease (GVHD). While differences in human leukocyte antigen (HLA) molecules between donor and host make a crucial contribution to the alloreactivity driving the donor–antihost response, the cytokine milieu consisting of molecules that both promote and regulate the alloresponse after transplantation is also critical. As such, genetic studies correlating donor and/or host cytokine polymorphisms with disease outcomes have provided useful insight into disease pathogenesis, often confirming effects that have been dissected in animal models of the disease. It is now clear that the polymorphic expression of key cytokines (particularly tumor necrosis factor and interleukin 10) has a demonstrable effect on disease outcome and overall transplant-related mortality. Consideration of the role of genetic polymorphisms in GVHD severity and procedural mortality associated with SCT will lead to improvements in patient outcome such that the addition of non-HLA genetic typing of potential donors will allow optimization of donor selection for a given recipient. This review provides a discussion of the current state of the literature regarding polymorphic expression of the key GVHD cytokines and their capacity to predict clinical disease outcome.