The procedural requirements of bone marrow transplantation (BMT) predispose to the dramatic induction of local and systemic inflammatory states and can be conceived in relation to transplant conditioning, the activation of alloreactive T cells and finally, the effector stage of graft-versus-host disease (GVHD). It is now clear that alloreactive T cell responses result in a dramatic and often fulminant amplification of systemic inflammation that is responsible for many of the characteristic causes of transplant-related mortality. The pathways by which inflammatory cytokines are induced after BMT and the resultant pathologies will be discussed.