BACKGROUND: Cypermethrins, possess eight isomers, used both as pesticide and as veterinary drug, were set different MRLs for livestock by CCPR and CCRVDF of Codex Alimentarius. Korea Food Code designates MRLs for livestock only as pesticide. METHODS AND RESULTS: This study presented necessaries of harmonization of MRL setting for compounds used both as pesticides and as veterinary drugs with regulatory aspects, showing an example of cypermethrin residue in livestock. CONCLUSION(S): For harmonization, following factors must be considered and recommended; designation of marker residue; alpha-cypermethrin, zeta- cypermethrin, and cypermethrin, clarification of the definition of target tissues; meat, fat, muscle, by-product, eggs, milk, and etc., method of analysis; clarification of target analytes of isomers, quantitation and calculation method as a principle of residue analysis.