Biflavonoids are flavonoid dimers that are much less studied than monomeric flavonoids. Their precise distribution among plants and their role in plants is still unknown. Here, we have developed a HPLC-DAD method that allows us to separate and simultaneously determine the five major biflavonoids (amentoflavone, bilobetin, ginkgetin, isoginkgetin, and sciadopitysin) in ginkgo (Ginkgo biloba L.). We performed tissue-specific profiling of biflavonoids in ten different plant parts: tree bark, twigs bark, twigs without bark, buds, leaf petioles, leaf blades, seed stalks, sarcotesta, nutshells, and kernels. We did not detect biflavonoids in plant parts not in direct contact with the environment (twigs without bark, nutshells, and kernels). We found the highest total biflavonoids content in leaves, where sciadopitysin was predominant. In contrast, in the bark, amentoflavone was the predominant biflavonoid, suggesting that more methylated biflavonoids accumulate in leaves and seeds. This is probably related to their biological function, which remains to be determined.