Despite many studies on non-HLA genetic polymorphism its role in transplantation is still not well understood. The NK cell receptor gene, MICA gene and Minor histocompatibility (mHag) system makes the puzzle still more intriguingly complex. Studies on cytokine gene polymorphism have enlightened some interesting associations such as the effect of donor IL-6 genotype on acute rejection in renal transplantation. In the bone marrow transplant where each polymorphism is taken as a risk factor for GVHD necessitates prospective testing of non-HLA gene polymorphism and hence, transplant outcome. Various typing methods are now available to identify the non-HLA genetic polymorphisms. A scenario can be envisaged where polymorphisms associated with transplant outcome are tested prior to transplantation at the same time as HLA typing.