In organ transplantation, ischemia/reperfusion injury is a multifactorial process that leads to organ damage and primary graft dysfunction. Injury to the organ is mediated by a complex chain of events that involves depletion of energy substrates, alteration of ionic homeostasis, production of reactive oxygen species, and cell death by apoptosis and necrosis. There is increasing evidence that mitochondria play a role in this process because of the profound changes experienced during ischemia and reperfusion. Understanding the mechanisms that lead to mitochondrial damage may be important for developing strategies aimed at improving graft outcome. In this review, we examine the role of mitochondria in ischemia/reperfusion injury and the possible mechanisms that may contribute to organ dysfunction.