During the last few decades, basic scientists and clinicians have gained a deeper insight of the cellular and molecular physiology of the immune system. The widespread application of molecular biology and genetic techniques has advanced our understanding of states of health and disease, bringing forth renewed hopes concerning the advent of a more "specific" therapeutic era of clinical immunology. The precise structural and genetic characterization of molecular complexes such as B and T-cell receptors, the Major Histocompatibility Complex (MHC), cytokines, chemokines, cellular receptors and co-receptors has produced a wealth of information open to both diagnostic and therapeutic purposes. We herein review several recent advances in the molecular and genetic characterization of immune deficiency states, autoimmunity and the induction of antigen specific immune unresponsiveness or tolerance, together with the therapeutic implications of these findings.