The complexity of sample matrices, coexistence of multiple forms of bioactive phytochemicals, and their interaction of with other cellular components pose a significant challenge for optimized extraction and accurate estimation of bioactive phytochemicals in foods and dietary supplements. This article discusses the significance of optimizing extraction procedures for accurate assay of phytochemicals from different matrices using bioactive isoflavones as model substrate because isoflavones are known to exist in nature as free aglycones or as conjugates with sugars and/or acids. The wide structural diversity and polarities of free and conjugated isoflavones makes optimum extraction and accurate quantification of isoflavones a challenging task. This paper reviews variables, extraction solvent composition (aqueous-organic solvents mixtures at different acidification levels), physical extraction techniques (Soxhlet, stirring, ultrasonic, microwave, pressurized, supercritical-fluid, high-speed counter-current chromatography), and parameters (temperature, pressure, number of cycles, solid-solvent ratio) that influence quantitative extraction of isoflavones from different matrices. In addition, this review covers a brief overview of structures, sources, bioactivities, separation, and detection used for isoflavones analysis. Optimum extraction efficiencies of isoflavones were obtained with EtOH : H (2)O : DMSO (70 : 25 : 5, v/v/v) as the extraction solvent and acidification of extraction solvent favored partial degradation of conjugated forms to their corresponding aglycones. Accurate quantification of isoflavones in foods, plants, and dietary supplements will allow researchers and regulators to provide more precise guidelines on dietary intake and safety levels necessary to achieve optimum health.