Advanced glycation endproducts (AGEs) form at an accelerated rate in diabetes and contribute to the development of macrovascular disease. Their precursors are detoxified by the glyoxalase system. Perturbations of the glyoxalase-1 gene may alter AGEs' interactions and affect pro-thrombotic factors. We screened the glyoxalase-1 gene for mutations and measured pro-thrombotic markers in 537 subjects from 89 healthy probands. Common single nucleotide polymorphisms (SNPs) were identified at positions -7 (C to T) and 20203 (C to A) from the translation start site. These SNPs were in Hardy-Weinberg equilibrium (CC=105, CA=266, AA=148; p>0.05; CC=126, CT=279, TT=114; p>0.05, respectively) and in linkage disequilibrium (D=27%, p<0.01), with mutant allele frequencies of 48% and 52% respectively. A significant association was found between SNPs at position 20203 and PAI-1 antigen concentrations and -7 and factor XIII A2B2 complex (p=0.001 and p=0.042). After Bonferroni correction a significant association remained between the SNP at 20203 and PAI-1 concentrations (p=0.005), and after adjustment for pedigree the association accounted for 1.3% of its heritability (p=0.04). No significant associations were found for SNP -7 T to C and factor VII activity, tPa concentrations, fibrinogen concentrations or factor XIII concentrations and SNP 20203 C to A and factor VII concentrations, PAI-1 concentrations, tPa concentrations or fibrinogen concentrations. Common variants in the glyoxalase-1 gene are associated with some pro-thrombotic factors, account for part of their heritability in healthy pedigrees and may alter susceptibility to macrovascular complications.