Ethnopharmacological relevance In Eastern Asia, E. koreanum Nakai (EKN) has traditionally been used as an aphrodisiac herbal medicine. However, there was no available information for its genotoxicity. This study was conducted to evaluate the genotoxic potentials of EKN. Materials and methods The phytochemicals of EKN were identified using liquid chromatography/tandem mass spectrometry (LC/MS/MS). Three standard battery of genotoxicity assay for bacterial reverse mutation, mammalian chromosomal aberration and in vivo micronuclei formation was employed. Results The LC/MS/MS analysis revealed four hydroxybenzoic acids, three lignans, and ten flavonoid glycosides in EKN. The bacterial reverse mutation assay revealed no mutagenic effects of EKN. Moreover, EKN did not show any clastogenic effects in the in vivo and in vitro assays. Conclusion EKN water extract was shown to be a non-genotoxic herbal medicine under the conditions tested in this study.