In recent years, increasing knowledge of the positive health effects of food polyphenols has prompted the need to develop new separation techniques for their extraction, fractionation and analysis. This article provides an updated and exhaustive review of the application of counter-current chromatography, high performance liquid chromatography, capillary electrophoresis, and their hyphenation with mass spectrometry to the study of food polyphenols. Flavonoids constitute the largest class of polyphenols, widely spread in the plant kingdom and common in human diet which has been the most widely studied with respect to their antioxidant and biological activities. The main subgroups are anthocyanins, catechins, isoflavones, flavonols and flavones. They are reported to exhibit antioxidant, anti-carcinogenic, anti-inflammatory, anti-atherogenic, anti-thrombotic, and immune modulating functions, among others. Since red fruit anthocyanins, soy isoflavones and flavanols from grapes and teas are currently the most used phenolic compounds for producing new nutraceuticals and functional foods, this review is focused on these three flavonoid groups.