The allogeneic mixed lymphocyte culture (MLC) has served as an important experimental system for elucidating the cellular and molecular basis of human lymphocyte responses. Complex mixtures of lymphocytes are stimulated by disparate alloantigens, inducing cellular activation and generating a cytokine milieu that is an excellent breeding ground for the proliferation and differentiation of many distinct lymphocyte subsets. Cloning of individual lymphocytes following alloactivation has allowed various cytotoxic lymphocytes to be isolated and characterized with respect to phenotype and specificity. These analyses have revealed that all types of cytotoxic effector cells are regulated by interactions with MHC-peptide ligands, however, the consequences of these interactions can result in opposite functional outcomes. In this review we summarize how allogeneic MHC class I-peptide ligands positively or negatively regulate the activities of four distinct groups of cytotoxic lymphocytes and how this information might be transferred into clinical use.