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Jasmonic acid (JA) is a plant hormone that mediates a wide variety of plant developmental processes and defense responses. One of the major roles of JA is the versatile enhancement of the production of secondary metabolites that function as second messengers in plant defense responses. Recently, several genes have been identified as coding for JA-responsive transporters involved in the membrane transport of various secondary metabolites. Although in the literature such transport activities have been explored by a number of methods, only a few studies systematically provide a detailed technical basis of the transport assay. Here, we describe the established method to functionally analyze secondary metabolite transporters by means of a yeast cellular transport system. Moreover, the advantages and disadvantages of the method are summarized and the relevant technical points are noted.