Quinoa was the traditional grain crop used by the prehispanic civilizations in America. Grains are white, black, yellow, and red-violet and plants are cultivated in vast areas of Peru, Bolivia and Ecuador. The recent description of the betacyanin pigment betanin in red-violet varieties is here further analyzed detecting the presence of amaranthin not previously identified in quinoa grains. Yellow-orange grains are characterized for the first time and up to four different betaxanthins are found to be responsible for this coloration. The native fluorescence of the identified betaxanthins makes the surface of the yellow quinoa grains glow with green fluorescent light. The presence of betalains is correlated with high antioxidant and free radical scavenging activities measured under the FRAP, ABTS and ORAC assays in grain extracts of 29 Peruvian varieties. TEAC equivalence is as high as 44.1 and 47.4 mmol Trolox/kg for the yellow and red-violet varieties analyzed respectively.