The bitter threshold concentrations for isoflavones for soy flake extract, soy protein isolate extract, and soy germ extract in water were 0.023, 0.023, and 0.039 µmol/ml. The saponin concentration of the soy flake extract, soy protein isolate extract, and soy germ extract at the threshold for milk were 0.115, 0.561, and 0.225 µmol/ml, respectively. The bitterness thresholds for isoflavones in the soy flake extract, soy protein isolate extract, and soy germ extract in milk were 0.338, 1.09, and 0.776 µmol/ml respectively, and the saponin concentrations at threshold were 0.115, 0.561, and 0.225 µmol/ml. Control, high oleic, and high cysteine soy flakes were analyzed for storage protein, functionality, isoflavone, and saponin content. The starting materials, when analyzed for original concentration of glycinin and f3-conglycinin by urea-SDS-PAGE, showed significant differences in storage protein compositions between the high oleic flakes and the other two flake varieties. The oleic flakes had 10% more glycinin, and 10% less f3-conglycinin than the control and cysteine flakes. The high oleic flakes yielded > 70% more total protein in the glycinin fraction than the other two varieties. The high cysteine flakes produced significantly higher purities of glycinin in the glycininrich fraction at 91 % compared to the oleic at 78% and control flakes at 87% purity The purity of the f3-conglycinin in the f3-conglycinin-rich fraction from the high oleic soybeans was 19%, with the major component of this fraction being glycinin. A purity of 74% for the B-conglycinin-rich fraction from the control flakes, and a purity of 67% for high cysteine flakes were observed. The control glycinin, intermediate and f3-conglycinin fractions all had higher solubilities than these fractions from the high cysteine and high oleic flakes The glycinin-rich fraction emulsification capacity for all flake varieties was significantly lower than the emulsification capacity of the f3-conglycinin-rich fraction The high oleic flake glycinin fraction showed better emulsifying capacity compared to the glycinin fractions of the other two varieties. In this study, in general, the control flakes contained a significantly higher concentration of isoflavones at 6.44 µmol/g than the high cysteine flakes at 5.23 µmol/g and v the high oleic flakes at 6.0lµmol/g. The mass yield of isoflavones for the control, high oleic, and high cysteine beans were 374, 398, and 389 µmoles, respectively. In general, the saponin concentration in the control, cysteine, and oleic flakes was 5.48, 5.46, and 3.74 umol/g, respectively. The mass yield of saponins for the control, high oleic, and high cysteine beans were 362, 209, and 319 µmoles, respectively.