In bread wheat (Triticum aestivum L), waxy genes are present at three loci (Wx-A1, Wx-B1 and Wx-D1) and are responsible for amylose synthesis in the grain. Near isogenic lines (NILs) of the agronomic cultivar Tremie with either one, two or three waxy null alleles were used to study the genome response to these null alleles through proteomic analysis of starch granule associated proteins of mature grain. Among the 352 spots that were revealed, 86 varied significantly between NILs. The main differences were observed for the granule bound starch synthase (GBSS), product of the waxy genes. A strong relation (R(2) = 0.94) between the amount of GBSS per gram of starch granule and the amylose quantity in the grain was revealed through quantification of the GBSS in each NIL The analysis of GBSS quantity for each NIL invalidated the additive hypothesis for the expression of this enzyme in (Wx-A1a Wx-D1a Wx-B1b) (Wx-D1a Wx-B1a Wx-A1b) and the normal form of Tremie. In addition, four proteins identified as inactive GBSS were increased (+144.9%) in the triple null isogenic form compared to the normal form of Tremie. The quantitative variations of the proteins present in starch granules support the idea of regulatory mechanisms between genomes.