Metabolism of the isoflavones biochanin A, genistein, formononetin, daidzein, equol and prunetin, the lignans matairesinol, secoisolariciresinol, enterodiol and enterolactone and the coumestan coumestrol was investigated to study the metabolism of phytoestrogens in dairy cows, and the possibilities to influence the content in milk. Four Norwegian Red Cows where allocated in a 4x4 latin square with four different silages. Silages had different botanical composition; red clover, botanical diverse, perennial ryegrass and timothy. The concentration of phytoestrogens was measured in feeds, omasum phases, feces, urine and milk by using the liquid chromatography (LC)-mass spectrometry (MS)/MS technique. Metabolism in reticulorumen and in digestive tract as well as apparent recovery in milk was calculated. Concentration of isoflavones was highest in red clover silage and lowest in timothy silage. For lignans it was the opposite. Phytoestrogens was extensively metabolized in reticulo-rumen. Biochanin A and genistein had the highest metabolism on the red clover diet and lowest on timothy. A number of unknown lignans was metabolized to the mammalian lignans enterodiol and enterolactone in the reticulo-rumen. When passing to omasum, isoflavones and coumestrol mainly followed large particles, while lignans was in greater extent evenly distributed between phases. Through the digestive system, differences in content of phytoestrogens between diets became smaller or disappeared. The concentration of isoflavones in milk was increasing with increasing intake. Red clover diet had the highest concentration of isoflavones in milk, with a dominance of equol. It appears that concentration of phytoestrogens in milk can be manipulated trough intake, but the effect is diminishing with increasing concentration in feeds.