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This study aimed to compare non-volatile metabolites and antioxidant activities of three purple radish varieties (cv. Sweet Baby, cv. Jungwoonmu, and cv. Boraking) leaves and roots. The total phenolic and flavonoid contents of the leaves were significantly higher than the roots. Glucosinolate content was significantly higher in the leaves than in the roots. In the purple radish roots, Boraking had the highest total anthocyanin content (420.14±16.2 mg cyanidin-3-glucoside/100 g) when compared to Sweet Baby (351.1±27.3 mg C3G/100 g) and Jungwoonmu (367.1±16.6 mg C3G/100 g). Based on the non-volatile metabolite analysis by liquid chromatography-electrospray ionization-quadrupole time-of-flight-mass spectrometry, 40 compounds, including flavonoid glycosides and coumaroyl glycosides in the leaves and 48 compounds, including various cyanidin glycosides and kaempferol glycosides in the roots were identified. Boraking was clearly classified from Sweet Baby and Jungwoonmu. The leaves of three purple radish cultivars had higher ABTS+ radical scavenging activity and ferric-reducing antioxidant power than the roots. The non-volatile metabolites and antioxidative activities of three purple radishes are expected to be used as basic information in food processing. In addition, the purple radish leaves, which are mostly discarded, will be used as a variety of food materials such as salads, wraps, and various vegetable-based dishes.