Over the last decades, the cultivation of fibrous flax declined heavily. There are number of reasons for that fact; one of them is flax susceptibility to the pathogen infection. Damages caused mainly by fungi from genus Fusarium lead to the significant losses when cultivating flax, which in turn discourage farmers to grow flax. Therefore, to launch the new products from flax with attractive properties there is a need to obtain new flax varieties with increased resistance to pathogens. In order to obtain the better quality of flax fiber, we previously generated flax with reduced pectin or lignin level (cell wall polymers). The modifications altered also plants' resistance to the Fusarium infection. Undoubtedly, the plant defense system is complex, however, in this article we aimed to investigate the composition of modified flax seeds and to correlate it with the observed changes in the flax resistance to the pathogen attack. In particular, we evaluated the content and composition of carbohydrates (cell wall polymers: pectin, cellulose, hemicelluloses and mucilage), and phenylpropanoid compounds (lignin, lignans, phenolics). From the obtained results we concluded that the observed changes in the vulnerability to pathogens putatively correlate with the antioxidant potential of phenylpropanoids accumulated in seeds, seco-isolariciresinol and coumaric acid diglycosides in particular, and with pectin level as a carbon source for pathogens. Surprisingly, relatively less important for the resistance was the physical barrier, including lignin and cellulose amount and cellulose structure. Certainly, the hypothesis should be verified on a larger number of genotypes. (C) 2014 American Institute of Chemical Engineers