Electron backscatter diffraction (EBSD) has been used for more than 30 years for analyzing the structure of minerals and artificial substances. In recent times, EBSD has been widely applied for investigation of irradiated nuclear fuel and matrices for the immobilization of radioactive waste. The combination of EBSD and scanning electron microscopy (SEM/EDS) methods allows researchers to obtain simultaneously data on a specimen’s local composition and structure. The article discusses the abilities of SEM/EDS and EBSD techniques to identify zirconolite polytype modifications and members of the polysomatic murataite–pyrochlore series in polyphase ceramic matrices, with simulations of Pu (Th) and the REE-actinide fraction (Nd) of high-level radioactive waste.