Heat shock proteins are families of highly conserved immunodominant molecules, reactivity to which has been implicated in the pathogenesis of a number of autoimmune and vascular disease states. However, heat shock proteins are cytoprotective, and in clinical and experimental arthritis, anti-heat shock protein reactivity can down modulate immune responses via a self-Hsp reactive, Th2-type mechanism. Despite a number of studies associating heat shock protein expression and anti-heat shock protein reactivity with allograft rejection, the balance between protective and damaging effects and the precise influence of these responses on graft outcome is unclear. This article reviews current knowledge surrounding heat shock proteins, autoimmunity, and allograft rejection and presents a perspective on the potential influence of these proteins and the stress response on allograft outcome.