The differences and similarities of endosperm microstructure in different places of vitreous and mealy kernels of wheat of different origin and hardness were evaluated. Kernels of seven T. durum and five T. aestivum cultivars of different origin, protein content, and mechanical resistance were investigated. Five points on kernel cross-section surface were selected for endosperm microstructure observation with scanning electron microscope JEOL 5200. Digital image analysis (DIA) was used for quantification of endosperm microstructure by transformation of the microscopic pictures and measuring of area and number of transformed image elements. Type of wheat (T. durum and T. aestivum), type of kernel (vitreous and mealy) and sampling place on cross-section surface influenced the endosperm microstructure statistically significantly. Despite high standard deviations within the data set for single kernel (from 5 to 25%), differences in vitreous and mealy kernels of particular wheat cultivars were evidently clear. Despite differences between vitreous and mealy kernels, types of wheat were very well classified in discriminant analysis. It should be said, however, that the differences in microstructure of mealy and vitreous kernels within the cultivar are smaller than those in the microstructure of different wheat types i.e. T. durum and T. aestivum.