The effect of protein on the thermal stability of isoflavones and the efficiency of their extraction from various soy matrixes was investigated. Isoflavones were extracted from soymilk, soybean. and soy protein isolate, varying in protein content and/or denaturation state, following nonenzyme-assisted solvent extraction or enzyme-assisted extraction. Selected samples were subjected to thermal treatment prior to and posthydrolysis of the protein. The extraction efficiency was a function of the enzyme used, sample to solvent ratio, protein content, and protein denaturation state. Proteolysis and reducing the sample to solvent ratio enhanced the isoflavone extractability, especially in samples with denatured protein. Results demonstrated clearly that the solvent extraction techniques currently used considerably underestimate isoflavone content in complex soy systems with high protein content. The stability of isoflavones was reduced upon protein hydrolysis, indicating that the protein moiety may have a protective effect against the thermal degradation of isoflavones.