Ischemia reperfusion injury is reviewed in the context of the evolution of flap research over the past decade. A description of the clinical relevance of this field is presented and the possible etiologies are reviewed. The pathophysiology of this injury is then explored in some detail. Both skin and myocutaneous flaps, in a variety of animal models, are discussed. Research performed in vitro, as well as in other organ systems similarly affected by ischemia and reperfusion, is also examined. Particular attention is placed on the function of several newly described inflammatory mediators where it appears relevant to future research and treatment in the field of reconstructive microsurgery.