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The objective of this work was to compare the contents of polyamines (putrescine, spermidine and spermine), and total soluble phenols and flavonoids in parts of plants grown under either organic or conventional cropping, commonly discarded during food preparation. The contents of free polyamines, total phenols and total soluble flavonoids in peels (zucchini squash, banana, potato, eggplant, orange, lime, mango, passion fruit and radish), leaves (zucchini squash, broccoli, carrot, collard, cassava, radish and grape), stalks (broccoli, collard and spinach) and zucchini seeds were analysed. Most analysed vegetables presented higher contents of polyamines and total phenols under organic cropping, contrary to the results obtained for total flavonoids, possibly because of the cultural practices adopted.