Over the past 20 years, consumption of soy beans, flax seeds and their products has grown steadily in western countries. Several epidemiological studies have shown that a regular diet consisting of products derived from these grains can reduce the risk of several chronic conditions including cardiovascular diseases, different forms of cancer, menopausal symptoms and bone density. It is stipulated that these benefits are due to bioactive compounds called phytoestrogens, a considerable number of these compounds have recently generated media exposure; consequently this has put tremendous pressure on regulatory agencies to monitor the quality of products. Specifically, the quantity and nature of active ingredients are determined in an effort to protect consumers from adulteration and fraud. This has led to the call for internationally-harmonized, rapid, sensitive, accurate, and reliable methods for phytoestrogens analysis in various food matrices, supplements and value-added specialty products. Also there is a need for methods to accurately determine phytoestrogens in biological fluids in order to understand the mode of actions for expected health benefits. In this review, we compiled recent advances (notably after 2000) on the effect of processing on the stability and nature of active products, physiological benefits of phytoestrogens, methods for extraction from a variety of food matrix, separations using GC and HPLC with detection by UV, DAD, CEAR, and MS. Current worldwide research on analytical methodologies which support a harmonized method for the detection of major phytoestrogens in soy products was discussed.