Research on the bioavailability of anthocyanins has focused, historically, on the non-flavonoid (C6-Cn) products that arise from anthocyanins in vivo. However, this review focuses on the products of anthocyanins that still possess the flavonoid structure (C6-C3-C6). Described herein are aspects of the in vivo pool of C6-C3-C6 anthocyanin-derived intermediates. Properties related to molecular size, shape, and polarity conveyed by six major anthocyanidin structures are discussed. The presence of a glycoside or not, and a variety of possible phase 2 conjugates, gives rise to a chemically diverse pool of C6-C3-C6 intermediates. Chemical properties influence the in vivo stability of anthocyanin-derived products, as well as their suitability as a substrate for xenobiotic conjugation and transport, and their association with the biomatrix. The flavonoid structure is associated with bioactivity and the particular properties of these C6-C3-C6 products of anthocyanins determines their deposition in the body, which may influence in vivo processes and ultimately health outcomes.