In recent years, the field of primary immunodeficienciency diseases (PID) has experienced remarkable progress with the identification of a number of new genes associated with specific diseases. Yet the diagnosis of PID remains difficult. In fact, this field requires continuous updating because once a novel molecule related to the immune function is discovered, the corresponding PID will soon be described. Since comprehensive reviews on the classification of PID are available, we concentrate here on reviewing some controversial and new issues, mainly those related to the role of T-cells and innate immunity. We will consider common variable immunodeficiency as an example of a PID where several immune pathways are impaired. We will also discuss the restricted usage of the T-cell receptor repertoire in PID. Innate immunity and Toll-like receptors (TLR) are new major players in this field. We will therefore discuss the association of TLR with the function of Bruton tyrosine kinase (Btk) that is essential in the development of B-cells and in the pathogenesis of X-linked agammaglobulinemia. Finally, we will discuss the role of mast-cells. These cells were once thought to be relevant almost exclusively to the pathogenesis of allergy. Now we know that mast cells are involved in initiating the adaptive response and may contribute to ineffective immune responses.