When discovered in the 50's, isoflavones were suspected to provoke infertility syndrome in sheep grazing on clover. Many others effects of these phytoestrogens have been documented afterwards. To determine the distribution of isoflavone metabolites in ewe tissues and look for a link with their physiological impact, two ewes were fed a diet containing 50% red clover silage (variety Pawera) for one month with a daily intake of 157.6 mg/kg bw of total isoflavones. Only aglycones were fed due to the fermentation stage of the silage. At the sacrifice, isoflavone metabolites and aglycones were analyzed in blood, liver, kidney, lung, heart, muscle, ovaries, uterus, mammary glands, suprarenal glands, thymus, aorta, thyroid, pituitary gland, cerebellum, olfactory lobes, and brain hemispheres using HPLC-Coularray and LC-MS-MS. The major compounds recovered in tissues were equol and daidzein, present as glucuronides. Kidney concentrations were 10-fold higher than in other tissues. Penetration in brain was very limited. Reproductive organs contained higher concentrations of isoflavones than heart, muscle, or thymus. Distribution of isoflavones in ewe tissues is unequal and may reflect specific impact in some target tissues.