The HPLC profiles of six fruits endemic of the VIII region of Chile were investigated using high resolution mass analysis (HR-ToF-ESI-MS). The anthocyanin fingerprints generated for the fruits were compared and the antioxidant capacities measured by the scavenging of the DPPH radical, the ferric reducing antioxidant power (FRAP), the superoxide anion scavenging activity assay (SA), and correlated with the inhibition of lipid peroxidation in human erythrocytes (LP) and total content of phenolics, flavonoids and anthocyanins measured by spectroscopic methods. Several anthocyanins were identified, including 3-O-glycosides derivatives of delphinidin, cyanidin, petunidin, peonidin and malvidin. Three phenolic acids (feruloyl-quinic acid, chlorogenic acid, and neochlorogenic acid) and five flavonols (hyperoside, isoquercitrin, quercetin, rutin, myricetin and isorhamnetin) were also identified. Calafate fruits showed the highest antioxidant activity. However, the highest LP activity was found for Chilean blueberries (>95%) followed by calafate fruits (91.27%) and luma (83.4%).