Introduction. Over the last years, the functions of the immune system have radically been revised. It has been illustrated how the different responses of the innate defense and the adaptative system were intimately intricated. State of knowledge. Innate immunity is an elaborate strategy, switched on by an invariant receptor-based response that is able to develop a specific defense against some pathogens. Moreover this innate immunity governs T- and B-cell-dependent adaptive immune response, mediated via dendritic cells whose maturation is controlled by immune specificity. The concepts of autoreactivity have also strongly progressed and the functions of the physiological autoimmune response have been highlighted. The notion of T- and B-cell self-antigens not only shapes the immune repertoire, but also the self-recognition process which is a tool for the control of the immune response itself. Perspective. New concepts of the pathophysiology of autoimmune diseases have emerged from a better understanding of the immune response, balancing between an intrinsic deregulation of the immune system and system deficiency to mount an effective response against an initial injury. Conclusion. Of course, therapeutic strategies are challenged by these data. We should expect that control of several autoimmune processes will be achieved in a few years, e.g. in rheumatoid arthritis or Crohn's disease controlled with biotherapies.