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The contents of bioactive compounds of quinoa (Chenopodium quinoa Willd.) are poorly known. We analyzed two isoflavones (daidzein and genistein) by HPLC in three local ecotypes of quinoa seeds from three different geographical and genetic regions in Chile: (a) Extreme North, with prevailing conditions of high temperature and dryness (local ecotype R49); (b) Center, with milder climate (local ecotype UdeC9); and (c) South, with cold, humid environment (local ecotype BO78). Genetic-driven differences among cultivars were tested by homogenizing the culture conditions of the three seed sources. In addition, seven commercial samples of quinoa purchased at local food markets were analyzed and compared to our experimental harvested seeds. In all samples daidzein content was higher than genistein (P < 0.05). The northern ecotype R49 exhibited higher content of isoflavones compared with the other two (UdeC9 and BO78), all grown under the same experimental conditions. Daidzein ranged from 1.15 (R49) to 0.70 (BO78) mg/100 g, while genistein varied from 0.25 (R49) to 0.05 (UdeC9) mg/100 g. Ecotype R49 had 1.6 and 1.7 fold higher daidzein contents than UdeC9 and BO78, respectively (P < 0.05). In the commercial samples, the daidzein/genistein ratio ranged from 25.2 to 3.9, daidzein ranged from 2.05 to 0.78 mg/100 g, and genistein ranged from 0.41 to 0.04 mg/100 g. To the best of our knowledge, this is the first report on the contents of daidzein and genistein in quinoa seeds. The study demonstrates that, besides its well-recognized nutritional value, quinoa possesses an excellent potential as a source of these health-promoting bioactive compounds. (C) 2013 Elsevier B.V. All rights reserved.