Soybeans are high in protein but also contain a number of minor constituents traditionally considered to be antinutritional factors. These include trypsin inhibitors, phytic acid, saponins and isoflavones. These compounds are now thought to have beneficial biological effects in the diet, such as lowering blood cholesterol or preventing cancer. Soybean processing changes the content of these minor constituents in various ways. This review discusses the changes in content of trypsin inhibitors, phytic acid, saponins and isoflavones as soybeans are processed into the conventional protein ingredients, flours, concentrates and isolates, as well as some of the traditional Oriental soybean foods.