Soy isoflavones are a phytochemical group of interest due to their possible health protective effects including reducing the risk of cardiovascular disease, lowering rates of prostate, breast and colon cancers, and improving bone health among many other claims. Much attention has been paid to the extraction and analysis of these compounds from foods since exact quantification is required to perform epidemiological studies and to establish their possible role in disease prevention. Unfortunately, analysis of isoflavones is a complicated procedure because there are several factors which may influence results, such as stability, incomplete recoveries during extraction, and difficult chromatographic separation of some chemical forms, among others. In this chapter, several aspects of isoflavone analysis in foods will be discussed, including sample conservation, sample preparation and analysis techniques. Special emphasis will be given to analysis techniques, separation and identification issues as well as the use of new technologies, such as UPLC and monolithic columns. Finally, different analysis protocols for the determination of these compounds in foods are proposed by combining different sample preparation and analysis techniques and methods available in the recent literature.