The objective of the study was to determine the antioxidant activity of flavones contained in skullcap (Scutellaria baicalensis Georgi) and procyanidines obtained from the bark of hawthorn (Crataegus oxycantha), as well as the extent of their degradation during the 20 minute baking of a shortcake at a temperature of 205° to 225°C. It was also examined whether or not the addition of fresh, dry roots of skullcap had a similar antioxidant effect as the impact of Commercial flavones. The antioxidant activity of polyphenols was different. The flavones contained in the skullcap appeared to be more active antioxidants if compared with the procyanidins of hawthorn, whereas the flavones more actively inhibited the formation of peroxides, secondary products of oxidation (TBARS), and conjugated dienes. The positive effect of the antioxidant activity of the skullcap flavones was measured with regard to the vitamins (α-tocopherol and β-carotene) contained in the shortcake, to fatty acids (in particular to acids belonging to the n3 and n6 groups of acids), cholesterol, and its oxidized derivatives. Two factors: baking time and high temperature during the baking of a shortcake had a negative effect of the stability of polyphenols, mainly on procyanidins isolated from hawthorn. Our investigations prove that it is possible to use freshly ground, dry skullcap roots to stabilize shortcakes against oxidation processes.