Muscle diseases include hereditary and acquired diseases with clinical manifestation in both childhood and adulthood. The different muscle diseases may have ultrastructural alterations that help us further understand the pathology of the disease. Specific changes in sarcomere structure help to classify a congenital myopathy. The detection of cellular aggregates supports the classification of myositis. Pathologically altered mitochondria, on the other hand, can occur both in genetic mitochondriopathies but also secondarily in acquired muscle diseases like myositis. Ultrastructural analysis of the myocardium is also helpful in the diagnosis of hereditary cardiomyopathies in childhood. This review article highlights the ultrastructural features of different muscle diseases and pathognomonic findings in specific disease groups.