Polyphenol compounds were analysed and storage stability determined of cold-pressed cakes from one non-genetically modified (non-GM) flax variety Linola and two GM lines: W92 line with overexpressed flavonoid biosynthesis pathway and GT line with overexpressed glycosyltransferase. The 20 g samples of each cake were stored in oxygen-free and dark conditions for 3 (T3) and 7 (T7) months at 4 and 21 °C. Initial (T0), and T3 and T7 samples were analysed for phenolic acids, phenolic acid glucosides and secoisolariciresinol diglucoside (SDG) content, and peroxide, free fatty acids and 2-thiobarbituric acid (TBA) values; total viable counts (TVC) and counts of yeast and moulds were also determined. At T0, T3 and T7, contents of all phenolic compounds were higher in both GM than non-GM cakes and in all cakes most of them were slightly decreased at T3 and more at T7. At T0 peroxide, free fatty acid and TBA values were lower in GM than in non-GM cake (particularly of TBA in W92 with the highest initial SDG content) indicating their better initial fat quality. Small changes of the indices reflecting fat deterioration during storage seemed, however, to be not dependent on polyphenol content. The TVC at T0, T3 and T7/4 °C were the smallest in W92 cake and did not change in a regular way in non-GM and GT cakes. Yeast counts were low in all cakes over the whole storage period and mould counts were the smallest in W92 cake. It may be concluded that protective properties of flax polyphenols, especially of SDG present in W92, were more apparent prior to than during cake storage.