Although histocompatibility testing and matching for histocompatibility leukocyte antigens (HLA) remains the "state of the art" for determining donor selection, non-HLA encoded genes such as those for minor histocompatibiity antigens also play an important role in determining haematopoietic stem cell transplantation (HSCT) outcome. Single nucleotide polymorphisms (SNPs) within the promoter regulatory regions of non-HLA encoded genes such as those for cytokines and cytokine receptors which regulate the production of such molecules may also play a role in determining the extent of post-transplant complications. Mannose binding lectin genes (MBL) and other genes such as those for myeloperoxidase (MPO) and Fcgamma receptor may aid in the control of infection post transplant. This review will summarise the latest research concerning this area of predicting HSCT outcome and indicate the potential clinical use of the results.