Lignans in flaxseed have been part of the human diet for centuries. In 1955, the isolation and structure of the lignan derivative secoisolariciresinol diglucoside (SDG) was reported. The biological role of SDG and mammalian lignan metabolites enterodiol and enterolactone was initially reported 20 years later. Experimental evidences showed the beneficial effects of lignans on breast, colon, and thyroid cancer. A modified gas chromatography/mass spectrometry (GC/MS) assay was developed for lignans in serum and colon samples of rats fed flaxseed meal. The method developed for the analysis of metabolites involves extraction and derivatization of samples and quantitative analysis by selected ion monitoring using GC/MS. The levels of lignan metabolites enterodiol and enterolactone were determined to be 0.013 and 0.23 microM in serum samples and 0.008 and 1.63 microM in colon samples.