Polyphenols such as flavonoids and stilbenes are abundant in our daily diet, and their roles in the protection and prevention of various diseases are substantial. However, the bioavailability varies among polyphenols and the actual compounds acting on the designated tissues are often not the native molecules consumed in the diet. Hereby, we review the bioavailabilty of the main classes of stilbenes and flavonoids, namely flavanones, flavones, isoflavones, flavanols, flavonols and anthocyanins, emphasizing on their absorption, distribution, metabolism and excretion (ADME). The bioavailability summary can be useful for future experimental design, especially the emphasis on the bioactivity on targeted tissues and organs. In addition, we review the bioefficacy of the polyphenols, emphasizing recent advances on health benefits both in vivo and in vitro. Other issues of importance, such as structure, food source and synthesis methods, are also considered.