With its two components, the immune system is equipped to fight with its best enemies, the microbes against which it was built. It does so vigorously, and it must be acknowledged, with an undeniable success. This does not prevent it from remaining vigilant between periods of open conflict. It ensures an immune surveillance against cancer cells that can appear without warning, but with mixed success. Sometimes, it aims at the wrong target, or it does not treat it as it should. It does too much or not enough. The enhancement of tumor growth, autoimmune diseases and allergies are examples of these “errors” of the immune system that becomes pathogenic, which is a problem for a defense system. The return of microbes is another problem: in the first decade of the twenty-first century, it was discovered that we harbor far more microorganisms than we have cells, and that they exert considerable influences on the immune system itself, as well as on the nervous system. Before this, it was thought that the immune system controlled the microbes; we learnt that it is the microbes that control the immune system. We will have to question this immune system.