Flax seeds are an excellent source of polyunsaturated fatty acids and high-grade protein. They are also rich in non-starch polysaccharides that are concentrated in their mucus cells. Flaxseed polysaccharides are soluble dietary fibres, which makes them an indispensable functional food ingredient. They can also serve as an additive, thus improving the structure of food, e.g. as a stabilizer, structure former, water and fat retention agent, etc. According to various researches, the functional and technological properties of polysaccharide flaxseed products are largely determined by the ratio of polysaccharide fractions and protein content, which depend on the production process. This research featured the effect of the method of obtaining flaxseed polysaccharide products on the protein content. The study employed chemical analysis and attenuated total internal reflection infrared spectroscopy (ATR-IR). The protein polysaccharide products under analysis were obtained by water extraction from two varieties of whole flax seed (Russia), under various conditions of treatment, cleaning, and fractionation. The conditions included pH, temperature, and process time. During water extraction of whole flax seeds, polypeptide-containing polysaccharide complexes were removed from the seed coats. The number, composition, and binding force between the peptide fragments and the polysaccharide matrix depended on the technological parameters of the process. The polysaccharide products were tested for total protein content. The results were consistent with the band intensity in the range of 1700–1500 cm–1, where protein carbonyl groups are usually manifested.