Isoflavones and lignans are biologically active plant-food constituents that have potential chemopreventive properties. Quantitation of isoflavones and lignans in humans is necessary to establish the benefits and risks of exposure to these compounds in populations and to determine which components of a mixed diet contribute to the exposure. Isoflavones and lignans are metabolized by colonic bacteria to more biologically active metabolites; thus both the parent compounds and the metabolites are measured routinely. Isoflavonoids (genistein, daidzein, dihydrodaidzein, O-desmethylangolensin and equol) and lignans (enterolactone, enterodiol, matairesinol and secoisolariciresinol) can be quantified in various body fluids. Typically, high concentrations of isoflavonoids in urine and serum are associated with soy consumption, and high concentrations of lignans are associated primarily with intake of whole grains and other fiber-containing plant foods. Controlled feeding studies and nutritional epidemiologic studies demonstrate a linear dose response between dietary intake and urinary excretion of isoflavones. Lignan excretion is associated positively with dietary fiber intake as well as with diets that are on average higher in fiber and carbohydrate and lower in fat; thus lignans have also been proposed as a marker of healthier dietary patterns. The complex interactions between the colonic environment and the external and internal factors that modulate it contribute to significant variation in serum and urinary phytoestrogen levels among individuals. Understanding these sources of variation is important to be able to use these measures effectively as dietary biomarkers.