Copao (Eulychnia acida Phil., Cactaceae) is an endemic species occurring in arid areas of northern Chile. The fruits are commercialized by peasants within the Elqui and Limari valleys and are appreciated for its acidic and refreshing taste. We now report the total phenolic (TP) and total flavonoid (TF) content, antioxidant activity, phenolic composition and main phenolic distribution in pulp and epicarp of copao fruits from different harvesting places from both valleys. The ascorbic acid content was determined in fresh fruit pulp, epicarp and juice. The phenolic-enriched extract was analyzed for antioxidant effect and composition. Ferulic acid, 9,10-dihydroxy-4,7-megastigmadien-3-one hexoside, isorhamnetin and quercetin glycosides were identified by HPLC-DAD-MS/MS analysis. The main compounds were isolated and fully characterized by NMR techniques. The main phenolic in the samples was isorhamnetin-3-O-[α-rhamnopyranosyl-(1→6)-β-glucopyranoside]. The HPLC pattern of the phenolic-enriched extracts of the fruits allows a differentiation of samples from the Elqui and Limari valleys. All fruit extracts and Amberlite-retained fraction from the methanolic extract were devoid of toxicity against human gastric AGS cells and human lung fibroblasts, with IC50 values >400μg/mL for AGS and 344 to >400μg/mL for fibroblasts, respectively. The compound identification, associated with the antioxidant activity and insignificant cell toxicity, adds relevant information for the possible development of this native fruit into a new crop. © 2014 Elsevier Ltd.