Pompe disease (acid alpha-glucosidase deficiency, OMIM 232300) is a rare lysosomal storage disorder due to autosomal recessive mutations in the GAA gene. It has also been called acid maltase deficiency and glycogen storage disease type II. There is a broad clinical presentation: the most severe form that presents in the first few months of life with cardiomyopathy and generalized muscle weakness that rapidly progresses to death from cardio-respiratory failure in the first year of life (infant-onset Pompe disease). A more slowly progressive disease, with little or no cardiac involvement, presents with proximal myopathy and/or pulmonary insufficiency, from the second year of life to late adulthood (late-onset Pompe disease). The recent development and introduction of enzyme replacement therapy with intravenous infusion of recombinant human acid alpha-glucosidase have made a major improvement in the morbidity and mortality of this disease. New therapies are also in development. With the availability of treatment, diagnostic methods have also improved, allowing for earlier recognition and potential early therapeutic intervention. The advent of newborn screening for Pompe disease may identify patients who can be treated before significant irreversible disease has occurred.