[en] Evidence for intimate interconnections between the three major systems of cell communication, the nervous, endocrine and immune systems, has opened important novel research perspectives. Neuroimmune-endocrine interactions are now established as crucial factors for the control of body development and homeostasis. In distant species and invertebrates, the foundations of both the neuroendocrine system and innate immunity were coexisting until now without any apparent problem. Some 400 millions years ago, in a relatively short period after agnathan fishes (e.g., hagfish and lamprey), adaptive immunity emerged in the first gnathostomes, cartilaginous fishes (e.g., shark and ray). Somatic recombination machinery characterizes adaptive immunity and is responsible for the random generation of the huge diversity of immune receptors able to recognize infectious antigens. The emergence of this novel form of immune defenses exerted a so potent pressure that structures and mechanisms developed along the paths of lymphocyte traffic to impose immunological self-tolerance, that is, the inability of the immune system to attack the host organism. Together with the generation of diversity and memory, self-tolerance constitutes a fundamental property of the immune system. The progressive rise in the level of immune diversity and complexity also explains why self-tolerance failures (i.e., organ-specific autoimmune diseases) were increasingly detected during evolution, the maximum being currently observed in the human species. The first thymus appeared in cartilaginous fishes (chondrichthyes), concomitantly with the emergence of rudimental forms of adaptive immunity. Though some forms of tolerance induction already takes place in primary hemopoietic sites (fetal liver and bone marrow), antigen-dependent B-cell tolerance is primarily due to an absence of T-cell help. Among all lymphoid structures, the thymus is the only organ specialized in the establishment of central self-tolerance. The thymus crucially stands at the crossroad between the immune and neuroendocrine systems. In this organ responsible for thymopoiesis—T-cell generation—(Kong et al., 1998), the neuroendocrine system regulates the process of T-cell differentiation from the very early stages. In addition, T lymphocytes undergo inside the thymus a complex educative process that establishes central T-cell self-tolerance of neuroendocrine principles (Geenen et al., 1992; Martens et al., 1996). Within the thymus, a confrontation permanently occurs between previously established neuroendocrine principles and a recent system equipped with recombination machinery promoting stochastic generation of response diversity. Contrary to a previous assumption, the thymus functions throughout life (Poulin et al., 1999; Geenen et al., 2003) and plays a fundamental role in the recovery of a competent T-cell repertoire after intensive chemotherapy or during highly active antiretroviral therapy (Mackall et al., 1995; Douek et al., 1998).