The amount of phenolic acids, flavonoids and betalains in Andean indigenous grains, quinoa (Chenopodium quinoa), kañiwa (Chenopodium pallidicaule) and kiwicha (Amaranthus caudatus), was determined. The total amount of phenolic acids varied from 16.8 to 59.7 mg/100 g and the proportion of soluble phenolic acids varied from 7% to 61%. The phenolic acid content in Andean crops was low compared with common cereals like wheat and rye, but was similar to levels found in oat, barley, corn and rice. The flavonoid content of quinoa and kañiwa was exceptionally high, varying from 36.2 to 144.3 mg/100 g. Kiwicha did not contain quantifiable amounts of these compounds. Only one variety of kiwicha contained low amounts of betalains. These compounds were not detected in kañiwa or quinoa. Our study demonstrates that Andean indigenous crops have excellent potential as sources of health-promoting bioactive compounds such as flavonoids. © 2009 Elsevier Ltd. All rights reserved.