Apoptosis is a key feature in the physiological and pathological regulation of the immune system. Concerning its central immunoregulatory roles, it would be reasonable to attempt to influence the progression of autoimmune diseases by pharmacological intervention in the processes of apoptosis. Numerous compounds capable of influencing apoptosis are known, but their exact mechanisms of action are only in part understood. The majority of the known chemicals does not affect apoptosis selectively, but alters the function of the whole organism, therefore considerable side-effects related to the application of these compounds may appear. The complexity of this situation is indicated by findings that the same compound can either induce or inhibit apoptosis depending on the experimental system and concentration studied. Our knowledge will, presumably, be extended in the future that could lead to the safer clinical application of these compounds. In this brief review article we attempt to present a synopsis of the most important agents influencing apoptosis in the immune system from a clinical point of view.