Danon disease, primary lysosome-associated membrane protein-2 (LAMP-2) deficiency, is histologically characterized by unusual vacuoles bound by membranes with sarcolemmal features in skeletal muscle. We studied skeletal muscle specimens from a male patient with genetically confirmed Danon disease who had two muscle biopsies, at age 20 months and 16 years, and from his mother with cardiomyopathy but without clinically apparent skeletal myopathy. In the patient, the number of vacuoles increased over the 14-year interval between biopsies, suggesting that the number of vacuolated fibers increases with age, and correlates with the development of muscle symptoms. In contrast, in the muscle biopsy from the mother there were no vacuoles even though she had decreased LAMP-2.