The content of anthocyanins, flavonols, and carbohydrates of Tropea red onions (Allium cepa L.) was determined by HPLC and HPLC-MS. Cyanidin derivatives constitute >50% of total anthocyanins, but delphinidin and petunidin derivatives, which have not been reported in red onions thus far, were also detected. The flavonoid distribution in the different layers of the bulbs indicates that, after homelike peeling, the edible portion contains 79% of the total content of quercetin 4'-glucoside but only 27% of the anthocyanins. Storage of onions for 6 weeks in different conditions, all of them mimicking home storage habits, resulted in a decrease to 64-73% of total anthocyanins. The same trend was verified for the total antioxidant activity, which was reduced to 29-36%. A decrease in glucose and fructose content correlated with anthocyanin degradation was also observed. Storage at low temperature seems to better preserve the onion anthocyanins.