This study was conducted to examine the effect of processing conditions (heating and homogenization combined with heating) and soy protein composition (by using selected Ontario soybean genotypes) on the colloidal structure of soymilk. The results revealed that heat treatment disrupted and denatured the large aggregates of soy proteins and decreased the particle size distribution of soymilk. Soymilks made from genotypes containing glycinin (11S) or group I (A 1, A2) of glycinin showed the larger loss in both protein and total solids compare to lines null in 11S. Unheated soymilks prepared from lines null for glycinin or lacking group I showed smaller particle size distribution. The protein subunit composition and ratio of 11S/7S had a significant effect on the development of soymilk gel structure. The gels made from lines containing group I (A1, A2) and group IIb (A3) of glycinin showed stiffer gels compare to the lines null in 11S. Results of this study can help to develop specific new soybean lines to meet consumer and industrial needs.