Phytoestrogens are plant-derived compounds with physiologic estrogenic effects. They are present in the plant as glycosidic conjugates, some of which contain further chemical modifications (acetate, malonate, and 3-hydroxy-3-methylglutarate esters and 2,3-dihydroxysuccinate ether). In the gastrointestinal tract, the conjugates undergo hydrolysis catalyzed by enzymes in the intestinal wall and by gut bacteria. On entering the systemic circulation, the phytoestrogens may undergo extensive metabolism to other compounds through reactions involving demethylation, methylation, hydroxylation, chlorination, iodination, and nitration. In addition, all these compounds can undergo conjugation to form beta-glucuronides and sulfate esters. This chapter describes the methods of analysis of all these compounds, the sources of or methods to manufacture suitable standards, and the procedures for examining the enzymes that catalyze these reactions.