Flavonoids, the most abundant polyphenolic compounds in foods, can be classified into flavanols, flavones, flavonols, flavanones, isoflavones and anthocyanidins. They have been demonstrated to possess strong antioxidant and disease-preventing properties especially for various degenerative diseases such as cancers and cardiovascular diseases in in vitro and in vivo models. However, flavonoids undergo metabolic transformation such as methylation, sulfation and glucuronidation, and consequently changes of their structures and biological activities. In order to reveal a relationship between parent compounds and their metabolites, the changes of structure and bioactivity of various flavonoids are reviewed in the vitro and vivo models.