In transplantation, activation of complement has largely been equated to antibody-mediated rejection, but complement is also important in recognition of apoptotic and necrotic cells as well as in modifying antigen presentation to T cells and B cells. As a part of the innate immune system, complement is one of the first responses to injury, and it can determine the direction and magnitude of the subsequent responses. Consequently, the effects of complement in allorecognition and graft rejection are increased when organs are procured from cadaver donors because these organs sustain a series of stresses from brain death, prolonged life support, ischemia and finally reperfusion that initiate proinflammatory processes and tissue injury. In addition, these organs are transplanted to patients, who frequently have been sensitized to histocompatibility antigens as the result of transfusions, pregnancies or transplants. Complement activation generates a series of biologically active effector molecules that can modulate graft rejection by directly binding to the graft or by modifying the response of macrophages, T and B cells of the recipient. However, complement is regulated and the process of regulation produces split products that can decrease as well as increase immune responses. Small animal models have been developed to test these variables. The guide for evaluating results from these models remains clinical findings because there are significant differences between the rodent and human complement systems.