Flavonoids are natural polyphenols that can be found in many vegetables, citric fruits and dietary supplements and are widely consumed worldwide in the human diet. Over the past 30 years, studies have demonstrated that these compounds present significant biological activities, and their antioxidant properties may be responsible for the prevention of many diseases such as neurodegeneration, atherosclerosis, tumor generation, and microbial infections. Moreover, studies have shown that flavonoids may be substrates of cytochrome P450 enzymes and undergo bioactivation to metabolites that inhibit tumor cell growth. Therefore, it is important to understand the CYP450-mediated metabolic profiles of polyphenolic compounds during drug discovery and development processes. This review highlights ligand-based and structure-based methods to predict the Phase I metabolism of polyphenols. Moreover, an integrated in silico approach for the prediction of Phase I metabolism of the flavonoids quercetin, rutin, naringenin and naringin, which provided useful information about the most likely metabolites of these flavonoids and their interactions with amino acid residues of CYP2C9, is described.