This report addresses the concept that permissible HLA mismatching, that is, mismatches that do not generate an allogeneic response, in hematopoietic stem cell transplantation (HCT) can be determined with structural similarity of polymorphic regions. We have applied the triplet version of a structural algorithm called HLAMatchmaker, which considers short sequences involving polymorphic amino acid residues on the molecular surface as key elements of immunogenic epitopes. The triplet matching effect was analyzed in a National Marrow Donor Program dataset consisting of 744 unrelated hematopoietic cell transplantation cases with 1 HLA-A, -B, or -C mismatch and 1690 fully HLA-A, -B, -C, -DR, or -DQ allele matched cases. In multivariate models adjusting for other significant clinical risk factors, the degree of triplet mismatching did not significantly correlate with patient survival, engraftment, or acute graft-versus-host disease (aGVHD). Other structurally based strategies should be pursued to identify permissible HLA mismatches in HCT.