The immune system of higher vertebrates consists of two components: innate and adaptive. The innate immune system relies on a set of germ-line encoded receptors that recognize conserved molecular patterns found only in microorganisms. The adaptive immune system uses somatically generated antigen receptors which are clonally distributed on the two types of lymphocytes: T cells and B cells. These antigen receptors are generated by random processes and, as a consequence, the general design of the adaptive immune system is based on clonal selection of lymphocytes expressing receptors with particular specificities. Here we discuss the essential role of the innate immune system in the clonal selection of lymphocytes and activation of the adaptive immune responses.