The effect of germination on isoflavone contents in two soybean varieties (Hutcheson and Caviness) was investigated. Soybean seeds were soaked at 25 degrees C for 12 h, germinated at 40 degrees C, and freeze-dried. The isoflavone contents of dry, soaked, germinated (hypocotyl length at 0.5, 2.5, and 6.5 mm), and nongerminated seeds were determined by high performance liquid chromatography. The maximum amount of total isoflavone, genistein, and daidzein with their beta-glucoside conjugates was obtained when hypocotyl length of the germinated-seed from var. Hutcheson was 0.5 mm (2.491, 1.500, and 0.671 mg/g), and from var. Caviness was 2.5 mm (2.78, 1.523, and 0.905 mg/g). A dramatic increase in malonylgenistin and malonyldaidzin (1.305 mg/g and 0.476 mg/g in Hutcheson, and 1.308 mg/g and 0.677 mg/g in Caviness, respectively) was observed at these hypocotyl lengths. A decrease was observed after this stage. Genistein and daidzein contents were highest just after soaking. Glycitein and its beta-glucoside conjugates remained almost the same during germination. Controlled germination can be used to enhance isoflavone content in soybean seed.