We examined differences in contents of flavonoids and terpene lactones, and their individual components in leaves of 54 ginkgo clones by high-performance liquid chromatography. We further analyzed the clusters of these ginkgo clones on the basis of the main medicinal components. We detected genetic variations among the ginkgo clones in terms of total flavonoids, terpene lactones, and their components. Furthermore, the variation coefficients were higher for components of terpene lactones than total flavonoids. We selected ginkgo clones with serial number 18, 42, 32, 50 on the basis of total flavonoid content and found increased content of quercetin, isorhamnetin, and kaempferol. Likewise, the content of terpene lactones (including ginkgolide A, ginkgolide B, ginkgolide C and bilobalide) was increased in clones with serial numbers 13, 42, 33, 51 and 65. From a comprehensive consideration of the components of clone leaves, clones with serial numbers 13, 65, 33, 51, 18, 32 and 42 could be popularized for planting for leaf use by grafting and cuttage or could be selected as breeding material for new ginkgo varieties used for their leaves.