Commercial potato and wheat starches were substituted to DS = 0.04 by cationic and anionic groups separately (to obtain cationic and anionic derivatives, respectively) and jointly (to obtain amphoteric derivatives). Microwave assisted processes were carried out in oven emitting radiation of 2450 MHz frequency and 0.5 W/g energy. Reaction products were examined by rheological methods, light, and scanning electron microscopy, and X-ray diffractometry. Nitrogen and carboxymethyl group contents were also determined. Incorporation of ionic substituents into the starch molecules significantly changes its physicochemical properties related to starch-water interactions, results in the decrease of the gelatinisation temperature, changes of the swelling characteristics, solubilisation and iodine complexation. The extent of these changes depends on type of processing (microwave or traditional) and starch species. Crystal and granular structures of investigated starches were only slightly damaged on derivatisation.