The paper presents a study on structure changes of waxy corn starches after physicochemical modification. The hydrothermal treatment (physical modifications) allowed to obtain pre-gelatinised starch (Merigel) or untreated starch of cook-up type (Resistamyl). Different degrees of cross-linking (low, medium and high) and medium level of substitution were the results of chemical modification of starch. The changes in the structure of modified starch were analysed with the use of the methods of low temperature nitrogen adsorption/desorption and of water vapour sorption. The BET equation was used to determine monolayer capacity (am) from isotherms of water vapour desorption, while the BJH equation was used to determine the surface area (SBJH), volume (VBJH) and mean diameter of pores (DBJH). Starches of the pre-gelatinisation type were characterised by SBETN2 values in the range of 0.18–0.45 m2/g, and starches of the cook-up type - 0.13–0.66 m2/g. Higher values of SBJH were noted for the cook-up starches (SBJH: 0.23–0.60 m2/g) in reference to the starches of the pre-gelatinisation type (SBJH: 0.12–0.32 m2/g). The medium degree of cross-linking of pre-gelatinisation type starches caused a lowering of the value of their monolayer capacity (am ads, am des), while for the cook-up type starches an increase of that value was observed, determined with adsorption and desorption water vapour isotherms. Porosity of the modified starch was determined with the use of mercury porosimetry. A decrease of porosity was noted for starch of the cook-up type (porosity 38.3–52.3%), compared to native waxy corn starch (59.3%). Starches of the pre-gelatinisation type (Merigel) were characterised by an increase of the value in question with increase in the degree of cross-linking: low ML (53.5%) < medium MM (59.2%) < high MH (65.7%). Starches of pre-gelatinisation type were characterised by pore volume (VMP) values in the range of 0.83–1.34 cm3/g, while starches of coo-up type had VMP values in the range of 0.57–0.79 cm3/g.