The immune system is a highly regulated, complex and integrated system which has evolved to provide the organism with substantial defenses against pathogenic organisms. Over the last several decades there has been an explosion of experimental data in this area, and new techniques in molecular and cellular biology have been crucial in deepening our understanding of immune processes. Most of these new techniques have allowed the isolation of the process or cell under study so that the results can be readily interpretable. At the present time, however, there is an emerging need to understand the system as it functions as a whole and the language of mathematics is the one best suited for this purpose. This review, written from the perspective of an experimental immunologist, describes some of the recent advances in the development of mathematical models of the immune system. Particular emphasis is placed on the rapidly growing field of modeling in HIV infection and T cell activation. Immunology as a whole will benefit from the introduction of the language of mathematics in much the same way as neuroscience has done in the last decade.