Electron microscopy is an important imaging tool to identify ultrastructural abnormalities of the myocardium, diagnose certain diseases, and expand the understanding of mechanisms of cardiovascular disease processes. Transmission electron microscopy (TEM) is still an important part of human cardiovascular pathology, but its use in veterinary medicine has become uncommon. Even in patients with minimal histopathological changes on light microscopy, there can be important ultrastructural findings that help to achieve a diagnosis. In addition, TEM can be valuable for research by shedding light on underlying mechanisms or investigating new forms of cardiomyopathies. This review highlights the importance of TEM, details normal and pathological ultrastructural findings, and provides insight into clinical and research uses. We also provide tips on tissue preparation, processing, and analysis that are key to successful use of this valuable tool.