Perforin, a pore-forming protein toxin synthesized and stored in the cytoplasmic vesicles of cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells, is secreted when these effector lymphocytes encounter virus-infected or neoplastic cells. Perforin is encoded by a single-copy gene and is critical for immune homeostasis and defense of the organism against intracellular sepsis. A complete deficiency of perforin expression in either mice or humans is associated with a syndrome of immune insufficiency and severely deregulated lymphoid homeostasis. Humans who inherit inactivating mutations of perforin or defects in various parts of the cellular machinery that delivers perforin to the target cell suffer from familial hemophagocytic lymphohistiocytosis (FHL), a fatal condition necessitating bone marrow transplantation, usually in infancy. In mice, a high incidence of spontaneous B cell lymphoma has also been noted as the animals age. Across human populations, a number of polymorphisms that result in measurable, but suboptimal CTL activity have been noted, and some of these predispose to attenuated FHL or susceptibility to infectious disease, but in many cases, to no discernible disease predisposition. This chapter discusses the significance of human perforin polymorphisms, particularly those associated with diseases other than FHL, and recent advances in our understanding of perforin biology and function.