Natural killer (NK) cells eliminate target cells infected with intracellular pathogens and tumor cells by employing the granule exocytosis and death receptor pathways. They also mediate the acute rejection of incompatible bone marrow cell (BMC) grafts. However, the cytotoxic mechanisms employed during acute BMC graft rejection are obscure. Throughout these studies, BMC graft rejection was compared between two inbred strains of mice: 129 mice, which apparently use perforin- and Fas-dependent cytotoxicity, and C57BL/6 (B6) mice, which are able to exploit perforin- and/or Fas-independent mechanisms. Using perforin-knockout (PKO) mice, we have determined that the granule exocytosis pathway can play a major role in NK cell-mediated rejection of allogeneic and MHC class I-deficient BMC, depending upon the genetic background of the recipient and the environmental housing conditions. Although the granule exocytosis pathway seems to be the most potent cytolytic mechanism of NK cell-mediated rejection, alternative perforin-independent mechanisms, such as death receptor-induced apoptosis, also exist. By preventing both perforin- and Fas-mediated interactions concurrently, we observed that 129 mice were impaired in mediating MHC class I-deficient BMC rejection, while B6 mice maintained strong rejection capacities. The administration of neutralizing TNF antibodies to B6PKO mice before challenging with Fas and MHC class I double-deficient BMC still did not reverse rejection. Thus, our studies reveal the relative importance of perforin-, Fas-, and TNF-based cytotoxicity in NK cell-mediated rejection of incompatible BMC.