Rye flours with extraction rate of 100% (wholemeal flour), 95% (brown flour), 90% (brown flour) and 70% (light flour) originated from Warko and Dańkowskie Złote rye varieties were prepared in order to compare the relation between flour extraction rates and content of bioactive compounds. The following compounds were analysed: total phenolic compounds (TPC), total flavonoids (TF), inositol hexaphosphate (IP6), reduced (GSH) and oxidised (GSSG) glutathione, tocopherols (T) and tocotrienols (T3). The reduced/oxidised glutathione status (GSH/GSSG) of the flours was examined as a potential index of flour resistance against oxidative stress. The following observations were made in relation to the flour types and bioactive compounds content of each variety: (a) milling process caused a decrease in the content of TPC, TF, IP6, GSH and GSSG, T and T3; (b) the most resistant to oxidation processes appeared to be brown flours, then light and finally wholemeal flour; (c) the ratio of tocotrienols to tocopherols (T3/T) was higher than that in rye flours with extraction rate of 100-90% whereas light flour was the poorest source of tocopherols and tocotrienols. The provided data on the contents of bioactive compounds in flour with different extraction rates strongly support the use of rye flours with extraction rates up to 90% in the bakery industry. It can be suggested that in the nearest future more and more rye products will be available on the market, especially those originated from wholemeal or brown flours.