We describe an isotope dilution gas chromatographic-mass spectrometric (GC/MS) method for the identification and quantitative determination of the lignans enterolactone, enterodiol, and matairesinol and the isoflavonoids daidzein, equol, O-desmethylangolensin, and genistein in feces. Following the addition of deuterated internal standards for all compounds, the feces samples are extracted and purified in several ion exchange chromatographic steps. Following formation of trimethylsilyl ethers, the samples are analyzed by combined capillary column GC/MS in the selective ion monitoring mode and corrected for all losses during the procedure using the deuterated internal standards. Results on the reliability of the method and values for nine Finnish omnivorous and nine vegetarian women are presented.