The transgenic potato clones of cultivar Irga with improved resistance to a necrotic strain of potato virus Y (PVYN) were subjected to heat treatment in order to determine their technological quality. The technological quality was determined on the basis of differences between mechanical properties of unmodified potato and transgenic clones during cooking and microwave heating. The compression test was applied in order to evaluate the mechanical resistance of raw, cooked and microwave-treated potatoes. Compression resistance was expressed by fracture stress F (kPa), fracture strain D (mm/mm), and Young modulus E (kPa). The differences in microstructure of potato tubers (unmodified and modified) were investigated using scanning electron microscopy (SEM). The observed differentiation in the mechanical properties of heat-treated potatoes was less connected with genetic modification but most of all with a kind of the process used. The heat processes caused a distinct decrease in mechanical resistance in all the examined tubers. However, the process of microwave heating resulted in more significant changes in mechanical properties of tubers than cooking. Deformation of parenchyma cells during cooking was directly connected with starch gelatinisation and gel formation. Microwave heating affected significantly cellular water evaporation which resulted in intercellular failure, collapsing of cells, and limitation of starch gelatinisation.