Soy isoflavones, such as genistein and daidzein, are bioflavonoids found in soy products that are able to interact with various hormones such as estrogen. In this article, a systematic review of published studies was carried out to investigate the characterization of isoflavones and their metabolites, sample pretreatment and quantitative analysis of isoflavones, and the influence of soy isoflavones on drug and xenobiotic metabolism. The results showed that aglycones with weak estrogen-like activities are the biologically active forms of the soy isoflavones in mammals. The most recent advances including extraction, purification and detection of isoflavones in soybean and soy products are discussed. The effects of soy isoflavones on drug and xenobiotic metabolism involve in regulation of phase I cytochrome P450 (CYPs) enzyme and phase I detoxifying enzymes expression and activity. At the molecular level, soy isoflavones have proved capable of estrogenic/antiestrogenic with tissue-selective, anti-cancer, anti-obesity, anti-oxidation, and tyrosine kinase inhibition activities. The authors conclude that soy isoflavones can decrease the incidence of many diseases and benefit for human health.