The paper presents a study on physicochemical and structure changes of waxy corn and tapioca starches after hydrothermal modification. It was found that with an increase of the degree of inhibition (low < medium < high) the viscosity of gels decreased. The process of inhibition slows down the retrogradation of starch gels, as opposed to native starches. Inhibited starches are characterised by a nearly 15% increase of the water solubility index. With increase in the degree of inhibition, tapioca starches are characterised by increasing values of surface area (SBET H2O), while for waxy corn starches it decreases. It was demonstrated that in the case of tapioca starches the differences in electron density distribution and SAXS scattering decrease with increase in the degree of inhibition (low < medium < high), and increase for the waxy corn starches. In the case of waxy corn starches, the capacity for iodine complexation decreased with low < medium < high degree of inhibition.