Cytotoxic T lymphocytes (CTLs) are cells of the immune system that recognize and kill cells that have been infected with intracellular pathogens, allogenic cells or tumor cells. It has been reported that CTLs participate in the pathogenesis of some autoimmune diseases. After stimulation with the antigen, CTLs undergo an activation process highly regulated, which leads to the cell to acquire an effector or memory function. In this review, we indicate the cellular markers associated with the different stages of CTL-differentiation (naive, memory and effector); we indicate the distinct models of CTLs differentiation; also, the mechanisms of CTLs cytotoxicity are mentioned. Furthermore, we describe the participation of CTLs in cancer and autoimmunity; the implications of CTLs in the progression of these diseases are discussed.