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The purpose of this investigation is to analyze for the Korean patent application trends of health functional foods based on the medicinal plant resources. An electronic search for health functional foods was conducted in WIPSON DB (https://www.wipson.com). Korean patents that were registered between January 1, 2008, and October 14, 2019, were selected in the present study. The principal applicants and organizations, target diseases and their technologies, the number of a valid patent, Korean, scientific, and medicinal names of medicinal plants and their classified patents were provided. A total of 1,404 patents were included in this study. The health functional food patents using medicinal plants applied to the disease content includes metabolic (477 cases, 34.0%), immune (143 cases, 10.2%), cutaneous (122 cases, 8.7%), neurodegenerative (97 cases, 6.9%), and musculoskeletal diseases (81 cases, 5.8%). The most patent applications in this study belonged to the Korea Food Research Institute (124 cases). The frequently intended medicinal plant families for the patent of health functional foods belonged to Asteraceae (33 species), followed by Fabaceae (15 species), Apiaceae (13 species), Rosaceae (12 species), Lamiaceae (10 species), Araliaceae (10 species). Panax ginseng C.A.Mey. (Ginseng Radix) was the most used for various diseases (12/18 classified patents). The patent information is useful for inventing new patent of health functional foods using medicinal plant resources. Moreover, these data should be connected in various research fields such as economic botany, herbal medicine, alternative, and complementary medicine.