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Fruit peels are the major by-product in fruit canned manufacturing and juices processing. The aqueous extracts of fresh and heat-drying peels of Psidium guajava (seed guava), Mangifera indica var. Chakonan (Chakonan mango), Citrus sinensis var. Navel (Navel orange) and Malus sylvestris (Granny Smith apple) were studied for qualitative total phenolic content (TPC) and total flavonoid content (TFC) as well as in-vitro antioxidant activity. Four antioxidant assays including Ferric Reducing Antioxidant Power (FRAP), 2, 2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activity, Beta-carotene bleaching and Oxygen Radical Absorbance Capacity (ORAC) were conducted in this study. All fresh extracts possessed significantly higher values in both TPC and TFC compared to the heat-drying extracts except for C. sinensis. They also showed higher antioxidant activity in all assays. Among the fruit peels, M. indica extract exhibited the strongest antioxidant activity. There were strong correlations between all antioxidant assays with TPC but weak correlations with TFC. Overall, this study provides supportive evidence for the superiority of M. indica peel as an excellent source of natural antioxidant and the consequence of heat-drying on their biological activities.