Effects of heat treatment and storage on quercetin and isorhamnetin content, major and minor components of isorhamnetin, and quercetin glucosides and aglycone, were investigated in onion (Allium cepa L.). The sweet onion 'Recorra' and red onions 'Hyred' and 'Red Baron' were cultivated in the south part of Norway and thereafter stored for eight months. The onions were either not field dried, but stored directly, or field dried and then stored, or field dried and then heat treated before storage. Neither storage nor heat treatment caused any major differences in total flavonol content in the investigated sweet onion as well as in the red onion cultivars. The two major quercetin glucosides differed in their changes in content during storage; quercetin-4'-glucoside did not show any consistent changes during storage in the two red cultivars, independent of treatment, whereas quercetin-3,4'-diglucoside increased significantly by 30 or 51%, respectively, during storage in 'Hyred' and 'Red Baron' in the 24 h heat treated onions. Isorhamnetin-4'-glucoside, which might possibly be of special interest from a human health point of view, was present at 2-3 times higher amount in the sweet onion cultivar than in the two red cultivars. Some of the quercetin glucosides present at lower concentrations, isorhamnetin-3,4'-diglucoside, quercetin-3,7,4'-triglucoside, and quercetin-7,4'-diglucoside, increased during storage in all treatments in both 'Hyred' and 'Red Baron', though sometimes a decrease was found at the end of storage.