This study identified and quantified five phenolic compounds, and evaluated the antioxidant capacity in vitro of fifteen native and exotic Brazilian fruit seeds that are typically discarded as waste. The contents of phenolic compounds were determined by ultra-performance liquid chromatography coupled with tandem mass spectrometry, and the antioxidant capacity was determined by oxygen radical absorbance capacity (ORAC) and 2,2-diphenyl-1-picrylhydrazyl (DPPH•) antioxidant assays. The results showed the antioxidant activity of Campomanesia pubescens, Hovenia dulcis Thunberg and Syzygium jambos (L.) Alston in the ORAC assay, and Hymenaea stigonocarpa, Hovenia dulcis Thunberg and Campomanesia pubescens in the DPPH• assay. Among the fifteen samples, four were highlighted regarding phenolic compound analyzes: Hovenia dulcis Thunberg (5.723 µg g-1) for gallic acid and myricetin (111.057 µg g-1), Passiflora edulis (1.208 µg g-1) for chlorogenic acid, Annona atemoya (1.0580 µg g-1) for vanillic acid, and Campomanesia pubescens (0.420 µg g-1) for ferulic acid. Therefore, these fruit seeds can be used as alternative sources of natural antioxidants.