The purpose of this research was to find out the effect of flour extraction rate on the antioxidative properties of traditional rye bread and then to compare the bioactive compounds content and antioxidant properties of rye breads with commercial wheat roll. Four types of rye flour with different extraction rates of 100 (whole meal dark flour), 95 (brown flour), 90 (brown flour), and 70% (light flour) originated from Warko rye cultivar were used for traditional bread baking with sourdough fermentation. Four types of the respective rye breads were analyzed for their potentially beneficial components, including tocopherols and tocotrienols, total phenolics and flavonoids, reduced glutathione, and inositol hexaphosphates. Moreover, the phenolic acids profile was provided. The Trolox equivalent antioxidant capacity (TEAC) of the breads was evaluated using free radical scavenging activities of 80% methanol extracts against ABTS*+ radical cation (ABTS radical cation decolorization method) whereas radical scavenging activity (RSA) was determined against 2,2-diphenyl-1-picrylhydrazyl radical (DPPH*). The superoxide dismutase-like activity (SOD-like activity) was evaluated as free radical scavenging activities of PBS extracts against superoxide anion radicals (O2*-). The results were compared to whole meal rye bread as well as to wheat roll taken as representative example of wheat based bakery product. The studies showed that flour extraction rates strongly affected the content of bioactive compounds and antioxidative properties of traditionally baked rye breads. The incorporation of the rye flours with extraction rates from 100 down to 70% in the formulation caused decrease in tocopherol (T), tocotrienol (T3), inositol hexaphosphate (IP6), and phenolic compound (TPC) contents in rye breads. No changes in reduced glutathione (GSH) contents were noted between each type of rye bread. A significant decrease in Trolox equivalent antioxidant capacity and radical DDPH scavenging activity was also found in bread formulated on flour with an extraction rate of 70% in comparison to the breads formulated on flour with extraction rates from 100 to 90%. The highest SOD-like activity was noted for rye bread formulated on flour with an extraction rate of 70%. The four types of rye breads showed better antioxidative properties and higher antioxidant contents when compared to wheat roll with one exception made to tocopherols and tocotrienols.