Soybeans include various functional food components, among which isoflavones are a subject of increasing research interest. During the production processes of tofu (bean curd), heating raw soymilk generates a lot of bubbles, in which saponin components can be detected in high concentrations. This chapter describes the basic concept essential for evaluating the functionality of soybean saponins; that is, the composition and content of soybean saponins are influenced by strain-specific and part-specific genetic polymorphism. Group A saponins (soyasapogenol A) are produced only in the hypocotyl (including the plumule and radicle parts) of the seed. This is probably because the gene producing soyasapogenol A expresses only at that location. The chapter shows the saponin components that each soybean variety, with respective genotype, produces in the cotyledon and the hypocotyl. Oral administration of soybean saponins provided antilipidemic effects when cholesterol was loaded and showed a synergistic effect, especially when these saponins were fed simultaneously with soybean proteins.