Harovinton, a variety of tofu type soybean, and 11 derived null soybean genotypes lacking specific glycinin (11S) and beta-conglycinin (7S) protein subunits were investigated to determine whether changes in protein composition affected the protein recovery in soymilk and its soluble fractions after various centrifugation steps. As both heating and homogenization have a marked effect on the increase in protein solubility, the changes occurring during these processing steps were studied for each soybean genotype. Harovinton and 11S-null genotypes showed significantly higher protein yields than the other genotypes evaluated. Subunits of group I (A(1), A(2)) of glycinin had a negative impact on protein solubility in all treatments, but this effect was the greatest in unheated soymilk samples. Samples containing a high beta-conglycinin to glycinin ratio showed an effect of heating on the solubility of the protein, as beta-conglycinin subunits aggregate with heating. The presence of the alpha' subunit of beta-conglycinin aids in the recovery of protein in the supernatant prepared from lines containing group I (A(1,4) A(2)) glycinin. The results of this study will help determine which specific protein composition will confer an increased stability in soymilk and soymilk-derived products.