Soy bean contain soy isoflavones which have an effect on different metabolic disorders in human. In this study we have analysed distribution of soy isoflavone between different product under recovery of soy protein. Using mass-spectroscopy and NMR analysis we have detected main isomers in soy bean daidzin and genistin. It was shown that isoflavone fraction is extracted to alcohol solution in processing of protein concentrate. Having analysed products of protein isolate processing we detected that isoflavones were extracted to alkaline solution during protein extraction. Only about 17 % of isoflavones have been remaining in protein isolate. Main part of them was detected in whey water after protein precipitation. And it is possible to elicit them according to standart procedure using extraction by ethylacetate and precipitation by chloroform. Taking into account our results we are proposing to use the by-products of soy protein processing for isoflavone concentrate producing.