We have correlated the clinical outcome with the level of HLA matching in 423 patients who received a transplant from a volunteer unrelated donor in the United Kingdom. HLA matching was performed at the allelic level (i.e. high-resolution) using reference strand mediated conformation analysis (RSCA) at HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1. The three-year probability of overall survival (OS) was 45% (median survival of 593 days; six-year overall survival probability was 40%). The mean follow-up was 1013 days (range 89-2697). Those matched for their HLA loci had a significantly better overall survival than the mismatched pairs (47% versus 40%, p=0.040). This result could be refined based on the number of alleles that were mismatched. In patients with a single HLA mismatch, the overall survival was 43%, compared to 30% in those with multiple mismatches; however, there was no statistically significant difference between matched pairs or those with one mismatch. Although there was no significant difference in the overall survival dependent on DPB1 matching in the group overall, in acute lymphocytic leukemia, DPB1-matched pairs had a significantly worse overall survival (log rank; p=0.025). Thus, a match for DPB1 is associated with a significantly increased risk of disease relapse, irrespective of the matching status for the other HLA molecules. In a multivariate analysis, a high pre-transplant levels of Tregs resulted in worse overall survival (relative risk (RR), 2.74; p=0.01), a trend to reduce disease-free survival (RR, 2.05; p=0.060) and to increase disease relapse (RR, 3.36; p=0.006). Residual patient CD4(+)CD25(hi) regulatory T cells may suppress graft-versus-tumour responses, decreasing the overall survival by increasing the rates of relapse. In acute leukemia, the presence of NOD2/CARD15 SNPs in the genotype of unrelated donor hematopoietic stem cell transplant pairs results in significant increases in disease relapse and consequently in death. These data show an important role for NOD2/CARD15 genotyping in transplantation and suggest a possible effect of the NOD2 protein in alloreactivity and tumour surveillance. Genotyping recipients and donors prior to transplant may present valuable information for planning and management of pre-transplant conditioning regimens, and for prognosis of the outcome.