Innate immunity is increasingly recognized as a major player in transplantation. In addition to its role in inflammation in the early post-transplant period, innate immunity shapes the differentiation of cells of adaptive immunity, with a capacity to promote either rejection or tolerance. Emerging data indicate that innate allorecognition, a characteristic previously limited to lymphocytes, is involved in allograft rejection. This review briefly summarizes the physiology of each component of the innate immune system in the context of transplantation and presents the current or promising therapeutic applications, such as cellular, anticomplement and anticytokine therapies.