A gradient reversed-phase high-performance liquid chromatography (HPLC) method has been developed to be suitable for the separation and determination of 12 isoflavones in soybeans. Profiles of daidzein, genistein, glycitein, and their malonyl-, acetyl-, and nonconjugated beta-glycosides were determined in cotyledons and hypocotyls of soybeans as affected by dry heating and germination. The results showed that the compositions and concentrations of isoflavones were remarkably different in the two parts of soybeans, and hypocotyls contained a much higher content of isoflavones than cotyledons (e.g., 7.8-fold higher). In hypocotyls, daidzein and its glycoside conjugates (59.6%) were the most abundant isoflavones, being followed by glycitein (26.6%) and genistein series (13.8%). In cotyledons, genistein and its glycoside conjugates (61.9%) were the main isoflavones, being followed by daidzein series (38.1%), and no glycitein series was found. Both hypocotyls and cotyledons contained remarkably high amounts of malonylglycosides (69.1 and 69.4%, respectively) and beta-glycosides (27.1 and 25.4%), and only a very small quantity of aglycones (3.8 and 5.2%) and no acetylglycosides were detected. Acetylglycosides and beta-glycosides were the thermal decarboxylation and deesterification products, respectively, of malonylglycosides, which were thermally unstable. The relative rates of decarboxylation and deesterification reactions were different in cotyledons and hypocotyls at different temperatures. During the process of germination, beta-glycosides decreased, and malonylglycosides and aglycones increased, and then, malonylglycosides were the major fractions in germinating soybeans. Interestingly, the present study occasionally found a significant circadian change between malonylglycosides and aglycones with a nocturnal increase of aglycones and decrease of malonylglycosides during germination, and even aglycones became the most abundant forms at night. However, this mechanism is yet to be investigated.