Electron microscopy has a strategic position in the diagnosis of neuromuscular disorders. In muscular fibers, the main abnormalities include vacuoles, inclusion bodies, and myofibrillar disorganization with or without abnormal inclusion material. Vacuolar changes include lipidic and glycogenic storage vacuoles, rimmed vacuoles, and lysosomal and autophagic vacuoles. Accumulation of abnormal inclusion material is found in nemaline myopathy, actinopathies, and hyaline body myopathy. Myofibrillar disorganization involves cores, multiminicores, and myosin chain depletion. Myofibrillar myopathies associate a pathologic pattern of myofibrillar dissolution and ectopic protein expression. They can be divided into two groups: myofibrillar myopathies with multiple expression proteins and myofibrillar myopathies with desmin and αB-crystallin expression only. In these two conditions, electron microscopy shows accumulation of a granulofilamentous material immunoreactive for desmin. At least three genes are implicated: desmin, αB-crystallin, and myotilin. Lastly, electron microscopy serves to identify changes, pathogenic or not, which are not shown up by light microscopy. Moreover, electron microscopy gives insight on pathophysiological mechanisms and can guide molecular genetics analysis.