Soy foods have attracted much attention for their possible effects on human health because of their phytochemical content, mainly isoflavones. Twelve forms of isoflavones have been identified in soybeans and soy products. Technological processes like heat treatment or fermentation can change the isoflavone profile of soy products. In this study, the effects of heat treatment and grain germination on isoflavone profile of soy milk prepared from BRS 213 soybean variety were evaluated. Isoflavone forms were separated and quantified by reversed-phase high-performance liquid chromatography. Heat treatment by autoclaving for 5 min did not affect the total isoflavone content, but led to a 90% decrease in malonyl forms, whereas β-glycosides increased by 70%. Autoclaving for 15 min led to a 20% loss of total isoflavones. Germination for 3 days did not change the total isoflavone content, but changed the distribution profile (15% increase of malonyl forms and 30% decrease of β-glycosides). Germination for 7 days increased the bioavailability of aglycone isoflavones in soy milk by seven times.