Herbal medicines have recently attracted much importance owing to the rising interest in their health benefits. Hence, further elucidation of the functions and mechanisms of these natural compounds is necessary. Our laboratory has established more than 30 kinds of monoclonal antibodies (MAbs) against bioactive natural compounds. Moreover, we have developed highly sensitive measurement systems for natural compounds, such as enzyme-linked immunosorbent assay (ELISA) and eastern blotting using MAbs. To expand the application of these MAbs to the functional analysis of natural compounds, we established a new approach for the isolation of the target compound from plant extracts using an immunoaffinity column conjugated with an anti-natural compound MAb. Through one-step purification using a MAb-conjugated immunoaffinity column, we have succeeded in preparing a knockout (KO) extract containing all components except the target compound, used as a hapten. Furthermore, we examined the pharmacological effects of the KO extract to identify the precise roles of the bioactive compound in the plant extract. To confirm another beneficial use of MAbs, we investigated the cellular localization and target molecules of natural compounds by immunocytochemistry (ICC) and Western blotting using MAbs. Our results demonstrated that MAbs clearly determined the cellular localization and target molecules of the natural compounds. These approaches may make it possible to determine the potential functions and target molecules of bioactive natural compounds in herbal medicines.