Development of a database of the soy isoflavone content of foods requires accurate and precise evaluation of different food matrixes. To evaluate accuracy, we estimated recoveries of both internal and external standards in 5 different soyfoods weekly. Standards were evaluated daily for system quality assurance. To evaluate sample precision, we analyzed soybeans and soymilk bimonthly for within-day precision and over 4 d for day-to-day precision. CVs should be < or = 8%. We validated our methods for single and multiple recovery concentrations by using our new internal standard, 2,4,4'-trihydroxydeoxybenzoin, and the external standards daidzein, genistein, and genistin. Concentrations of 12 isoflavone isomers, 3 aglycones (daidzein, genistein, and glycitein), and 9 glucosides (daidzin, genistin, glycitin, acetyldaidzin, acetylgenistin, acetylglycitin, malonyldaidzin, malonylgenistin, and malonylglycitin) were measured in a variety of soybeans and soyfoods. The extraction methods used depended on soyfood type. The HPLC conditions for soy isoflavone analysis were improved, leading to good separation with a short analysis time (60 min/sample). A data bank of concentration and distribution of isoflavones in different soybean products was assembled. A wide range of isoflavone concentrations, from < 50 microg/g to > 20,000 microg/g, was found in different soy products. The glucoside forms are almost twice the molecular weight of the aglycones; reported isoflavone concentrations should be normalized to the aglycone mass (or an isoflavonoid equivalent) rather than a simple sum of all isomers.