MHC typing for human hematopoietic cell transplantation (HCT) from unrelated donors is currently performed by using a combination of serologic and molecular techniques. It has been determined that allelic differences in human MHC molecules, revealed by nucleotide sequencing but not by serologic typing, substantially influence graft rejection and graft-versus-host disease, two serious complications of clinical HCT. We studied transplantation of purified hematopoietic stem cells in a series of mouse strains that were matched at the MHC but had different background genes, and we observed striking differences in engraftment resistance and graftversus-host disease severity, both factors depending on the donorrecipient strain combination. The individual mouse lines studied here were established nearly a century ago, and their MHC types were determined exclusively by serologic techniques. We considered the possibility that serologically silent MHC polymorphisms could account for our observations and, therefore, we performed DNA sequencing of the class I and II MHC alleles of our mouse strains. At each locus, exact homology was found between serologically MHC-matched strains. Our results likely extend to all serologically MHC-matched mouse strains used in modern research and highlight the profound and variable influence that non-MHC genetic determinants can have in dictating outcome after HCT.histocompatibility antigens ͉ hematopoietic stem cell transplantation I n clinical allogeneic hematopoietic cell transplantation (HCT), matching of donors and recipients at the MHC is considered essential to minimize graft-versus-host disease (GVHD) and graft rejection. Related donors are usually siblings who have inherited the same parental alleles and thus encode MHC molecules (designated HLA in humans) genotypically identical to the patient. Because related donors are often unavailable, MHC-matched unrelated donors are sought by volunteer bone marrow (BM) donor registries. Historically, human MHC typing has been performed by using panels of alloantibodies derived from individuals exposed to HLAs by pregnancy or transfusion (1). In the last decade, such serologic typing has given way to the more precise DNA-based technology, which has revealed that in Ͼ20% of serologically matched unrelated donors, sequence polymorphisms exist in class I and͞or class II MHC molecules (2-7). Thus, serologically defined HLAs can encode families of alleles whose differences are distinguishable only by DNA-based typing methods. These polymorphisms encode amino acid substitutions that cluster within the MHC peptide binding groove and, although serologically silent (2, 8), can influence T cell activation. It has been shown in human HCT that the consequences of these serologically undetectable differences include increased risks of GVHD and mortality when the disparities are in the MHC class II loci (7, 9) and increased graft failures in the cases of MHC class I disparities (2, 3, 10).Polymorphisms at non-MHC genes encoding for minor histocompatibility ...