Transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) are popular and powerful techniques used to characterize heterogeneous catalysts. Rapid developments in electron microscopy – especially aberration correctors and in situ methods – permit remarkable capabilities for visualizing both morphologies and atomic and electronic structures. The purpose of this review is to summarize the significant developments and achievements in this field with particular emphasis on the characterization of catalysts. We also highlight the potential and limitations of the various methods, describe the need for synergistic and complementary tools when characterizing heterogeneous catalysts, and conclude with an outlook that also envisions future needs in the field.