The isolation of water-soluble polysaccharides and proteins solubilized during the treatment of rye flour in an isotonic aqueous medium is described. Protein and polysaccharide assays of the aqueous fractions showed the high extraction performance of these compounds. Then, nanoparticles were synthesized from these hydrophilic isolates using fluorescein as a model drug and sodium hexapolyphosphate as a cross-linker. The preparation process consisted of dispersion, desolvation, drug incorporation, crosslinking and separation of nanoparticles. The physicochemical analysis revealed that nanoparticles were successfully synthesized with rye hydrophilic isolates using a desolvation method. These studies demonstrated that rye nanoparticles are a promising candidate as an active compounds vehicle system.