A combination of high-pressure extraction and preparative chromatography was used to purify the group A and group B soyasaponins from soy germ for use as analytical standards and for use in biological assays. A standardized sample preparation and extraction method was developed for the analysis of phytochemicals found in soy and processed soy products, which is reproducible in other laboratories. The extracts can be analyzed with standard liquid chromatography-mass spectrometry and high-performance liquid chromatography methods to identify and quantitate the group A and group B forms of the soy saponins, as well as the soy isoflavones. Complete saponin analysis of the extracts prepared from soy germ (hypocots), hulls, and cotyledons shows that a significant portion of the saponins is concentrated in the germ. The germ contains nearly all of the group A soyasaponins, while the group B soyasaponins are nearly equally distributed between the germ and the cotyledons. The hulls contain little of either isoflavones or saponins. Whole (full fat) soybeans grown on a tract in central Illinois in 2003 contain approximately 4-6% saponins on a weight basis, of which about one-fifth or less of the total saponin content are group A soyasaponins; the balance is group B soyasaponins.