High-performance size exclusion chromatography was used to separate soybean extracts. The separation of the major storage proteins, including glycinin and beta-conglycinin, was determined by analysis of the subunits on sodium dodecyl sulfate gel electrophoresis, The extracts of defatted flour and whole beans showed a high degree of polymerization of the storage proteins. Addition of a disulfide reducing agent (dithiothreitol) resulted in a decrease of the polymerized forms. The separation of the major glucoside isoflavones (genistin, daidzin, and glycitein 7-beta-glucoside) was determined. The isoflavone glucosides eluted well past the elution time of a: small totally included molecule, indicating that they are separating by mechanisms other than size exclusion. Size exclusion chromatography was used to monitor the separation of the soybean extract in an aqueous two-phase extraction system. The major storage proteins partitioned to the salt phase, and the isoflavones and other hydrophobic compounds partitioned to the poly(ethylene glycol) phase.