Aims: To compare endogenous beta-glucosidases and beta-galactosidases for hydrolysis of the predominant isoflavone glycosides into isoflavone aglycones in order to improve biological activity of soymilk. Methods and Results: beta-glucosidase and beta-galactosidase activities of probiotic organisms including Lactobacillus acidophilus ATCC 4461, Lactobacillus casei 2607 and Bifidobacterium animalis ssp. lactis Bb12 in soymilk were evaluated and correlated with the increase in concentration of isoflavone aglycones during fermentation. The concentrations of isoflavone compounds in soymilk were monitored using a Varian model high-performance liquid chromatography (HPLC) with an amperometric electrochemical detector. In all micro-organisms, beta-glucosidase activity was found greater than that of beta-galactosidase. There was an increase in the aglycone concentration with incubation time because of the apparent hydrolytic action on isoflavone glycosides. Aglycone concentration in the soymilk with L. acidophilus 4461, L. casei 2607 and B. animalis ssp. lactis Bb12, increased by 5.37-, 5.52- and 6.10-fold, respectively, after 15 h of fermentation at 37 degrees C. The maximum hydrolytic potential was also observed at 15 h of fermentation for the three micro-organims coinciding with peak activities of the two enzymes. Conclusions: beta-glucosidase activity was more than 15 times higher than beta-galactosidase activity in soymilk for each of the micro-organisms during fermentation. beta-glucosidase played a greater role in isoflavone glycoside hydrolysis. Significance and Impact of the Study: Screening for beta-glucosidase and beta-galactosidase activities among probiotics in soymilk is important for the improvement of biological activity of soymilk and in the selection of micro-organisms for use in the growing industry of functional foods and beverages.