Lignans and isoflavonoid phytoestrogens, produced from plant precursors by colonic bacteria, may protect against certain cancers. We examined the effects of flaxseed consumption on urinary lignans and isoflavonoids. Eighteen women consumed their usual omnivorous diets for three menstrual cycles and their usual diets supplemented with flaxseed powder (10 g/d) for three cycles in a randomized crossover design. Three-day urine samples from follicular and luteal phases were analyzed for lignans and isoflavonoids by isotope-dilution gas chromatography-mass spectrometry. Excretion of the lignans enterodiol and enterolactone increased with flaxseed from 1.09 ± 1.08 and 3.16 ± 1.47 to 19.48 ± 1.10 and 27.79 ± 1.50 μmol/d, respectively (P < 0.0002). Enterodiol and enterolactone excretion varied among subjects in response to flaxseed (3- to 285-fold increase). There were no differences in excretion of isoflavonoids (daidzein, genistein, equol, and O-desmethylangolensin) or the lignan matairesinol with flaxseed. Excretion was not altered by phase of menstrual cycle or duration of flaxseed consumption.