Identification of isoflavone glycosidic conjugates from several soy products was carried out by HPLC-mass spectrometry. Positive ion mass spectra obtained using the heated nebulizer-atmospheric pressure chemical ionization interface gave the most sensitive and structurally useful information about each isoflavone conjugate. Although extraction of isoflavones from soy products with 80% aqueous methanol at room temperature was just as efficient as at 60-80 °C, extraction at higher temperatures caused changes in isoflavone composition and should be avoided. Soybeans and defatted soy flour (which had been minimally heated during their preparation) contained mostly isoflavone 6″-O-malonylglucoside conjugates, with lesser quantities of the β-glucosides and only trace amounts of 6″-O-acetylglucoside conjugates. Soy milk, tofu, and soy molasses, each of which involves heating to 100 °C during their manufacture, contained mostly isoflavone β-glucosides. Toasted soy flour and an isolated soy protein had moderate amounts of each of the isoflavone conjugates. © 1994, American Chemical Society. All rights reserved.