The relation between high molecular weight glutenin subunit alleles and flour quality traits have been studied for 117 recombinant inbred lines (RILs) derived by single seed descend to F7 from a cross of Anza, a low quality cultivar, and Inia, a high quality cultivar, containing different alleles at 3 GLU-1 seed storage protein loci. RILs were classified by SDS-PAGE for the 8 possible combinations of the alleles. The allelic variation at the GLU-D1 locus accounted for most of the variation observed in SDS-sedimentation, mixing time and tolerance, and protein content. The GLU-D1 allele encoding the subunits 5+10 was superior to its allelic counterpart, encoding 2+ 12. All three loci had significant single locus additive effects for SDS-sedimentation volume and mixing tolerance. The additive effects of GLU-D1 locus on mixing time and protein content were also significant. The epistatic additive effects were mostly negative and with the exception of αAB and αAD for SDS-sedimentation volume were not significant.