The results of investigations into interfaces and thin films in heterostructures with the use of spherical-aberration-corrected transmission and scanning transmission electron microscopy (STEM) by applying supersensitive energy-dispersion X-ray microanalysis are presented. Using examples of heterostructures of various materials (Si/Ge, InGaAs/InAs, AlN/GaN, YBCO on various substrates and LuFe(Co)O₃/YSZ), the possibility of determining the morphology and atomic structure of interfaces and mechanisms of the formation of layers is shown.