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Four species of edible tubers endemic to and domesticated in the Andes, native potato (Solanum sp.), mashua (Tropaeolum tuberosum Ruiz & Pavón), oca (Oxalis tuberosa Molina) and ulluco (Ullucus tuberosus Caldas), were studied for their antioxidant capacity and associated secondary metabolites. The antioxidant capacity was measured using ABTS − radicals and total phenolics, carotenoids, anthocyanin, betaxanthin and betacyanin content were also characterized. The antioxidant capacity found in the crops studied ranged from 483 to 9800 µg trolox equiv. g −1 , phenolics ranged from 0.41 to 3.37 mg chlorogenic acid equiv. g −1 , anthocyanins ranged from 0.08 to 2.05 mg cyanidin 3-glucoside g −1 and carotenoids ranged from 1 to 25 µg β-carotene g −1 . The content of bioactive compounds was high and variable between crops and within the genotypes studied. In general, mashua tubers showed the highest antioxidant capacity and phenolic, anthocyanin and carotenoid content compared with other crops. Ulluco was the only crop that contained betalains in the acid form of betaxanthins (22-96 µg g −1 ) and betacyanins (64 µg g −1 ) with no presence of carotenoids or anthocyanins. This is the first publication regarding the antioxidant capacity of and associated secondary metabolites in Andean tubers. This information can be useful in the identification of Andean tubers species and genotypes with potential value as a novel dietary source of antioxidants for food, and also for medicinal use.