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Many dark-colored fruit juices, rich in anthocyanins, are thought to be important for human health. Joboticaba (Myrciaria cauliflora) fruits, native to Brazil, have phenolics including anthocyanins and are processed into juice and other products. The phenolic constituents in the fruits of jaboticaba were studied by high-performance liquid chromatography coupled with electrospray ionization time-of-flight mass spectrometry. Twenty-two compounds were identified or tentatively determined by detailed analysis of their mass spectral fragmentation patterns; 11 compounds including 7 gallotannins, 2 ellagic acid derivatives, syringin, and its glucoside were detected for the first time in the fruit. The compositional differences among the fruit extracts and their commercial products were also compared by principal component analysis; two anthocyanins, delphinidin 3-O-glucoside and cyanidin-3-O-glucoside, as well as two depsides, jaboticabin and 2-O-(3,4-dihydroxybenzoyl)-2,4,6-trihydroxyphenylacetic acid, present in the fruit extracts were not detected unexpectedly in commercial jaboticaba juice or jam. Therefore, the stability of anthocyanins in jaboticaba fresh fruits and products has been compared directly with that of other dark-colored fruit products made from blueberry and Concord grape, and the same trend of decreasing amounts of anthocyanins was observed in all tested products. The antioxidant activities (DPPH(•) and ABTS(•+)) of jaboticaba fresh fruit extract and commercial samples were also compared. Principal component analysis proved to be a useful way to discern changes between fresh and processed fruits. Jaboticaba is a promising fruit with antioxidant capacity similar to those of other so-called superfruits; however, during processing the levels of some of anthocyanins and other polyphenols decrease significantly, and therefore the capacity of these products to affect human health may vary significantly from that of the fresh fruit.