Hereditary myopathies characterized by the development of autophagic vacuoles can be categorized into three groups: rimmed vacuolar myopathies, acid maltase deficiency (glycogen storage disease type II), and myopathies characterized by the autophagic vacuoles with unique vacuolar membranes. Rimmed vacuolar myopathies are most likely secondary lysosomal myopathies because all of the identified causative genes encode extralysosomal proteins. Deficiency of acid maltase, a lysosomal enzyme, has been well characterized clinically, pathologically, biochemically, and genetically, and may become treatable in the near future. The diseases in the last category are relatively rare, but appear to be genetically heterogeneous and the list of these diseases is expanding. Danon disease, the best-characterized disorder in this group, is caused by primary deficiency of a lysosomal membrane protein, LAMP-2. Therefore, diseases in this category are expected to be primary lysosomal disease.