Soybean is a major source of protein and other nutrients and non-nutrient bioactives for human health. The objective was to compare the bioactive compounds of a low-protein (BRS 133) soybean in comparison to a high-protein (BRS 258) soybean cultivar. The high-protein soybean contained 17% lower carbohydrates and a lower chemical score (63) in relation to the low-protein soybean, which had a higher chemical score (76), associated with the higher methionine content (1.2%). Cultivar BRS 258 had more calcium (15.5%), phosphorus (30.1%), iron (18.7%), copper (9.0%) and zinc (11.5%), and a higher concentrations of lunasin, BBI and lectin (20.3%, 19.0% and 27.1%, respectively) than the low-protein cultivar. BRS 133 had 75.4% higher concentration of total isoflavones (5.1% of total aglycones) and 31.0% total saponins, as compared to BRS 258. It was concluded that the low-protein soybean cultivar contained higher isoflavones and saponins, but lower levels of minerals and bioactive peptides, such as lunasin. © 2009 Elsevier Ltd.