Isoflavones are recognized to be estrogenic compounds that are often associated with a reduced risk of cancers. The estrogenic activity can be enhanced after metabolization to more active compounds such as genistein and daidzein by gut microorganisms. The direct use of these metabolites has been investigated in laboratory rats and farm animals over the last decade. This paper reviews the research progress on the effect of isoflavonic compounds including metabolites on the physiology, gut microbiology and performance of farm animals in China.