Glycogen storage diseases (GSDs) are a group of rare, monogenic disorders that share a defect in the synthesis or breakdown of glycogen. This Primer describes the multi-organ clinical features of hepatic GSDs and muscle GSDs, in addition to their epidemiology, biochemistry and mechanisms of disease, diagnosis, management, quality of life and future research directions. Some GSDs have available guidelines for diagnosis and management. Diagnostic considerations include phenotypic characterization, biomarkers, imaging, genetic testing, enzyme activity analysis and histology. Management includes surveillance for development of characteristic disease sequelae, avoidance of fasting in several hepatic GSDs, medically prescribed diets, appropriate exercise regimens and emergency letters. Specific therapeutic interventions are available for some diseases, such as enzyme replacement therapy to correct enzyme deficiency in Pompe disease and SGLT2 inhibitors for neutropenia and neutrophil dysfunction in GSD Ib. Progress in diagnosis, management and definitive therapies affects the natural course and hence morbidity and mortality. The natural history of GSDs is still being described. The quality of life of patients with these conditions varies, and standard sets of patient-centred outcomes have not yet been developed. The Nature Reviews Disease Primers | (2023) 9:46 2 0123456789();: Primer caused by genetic defects that are associated predominantly with abnormalities of glycogen metabolism and that are recognized in the literature as GSDs, namely, GSD 0a, GSD 0b, GSD I, Pompe disease, GSD III, GSD IV, GSD V, GSD VI, GSD VII, GSD IX, GSD X, GSD XI (lactate dehydrogenase sub unit A deficiency), GSD XII, GSD XIII, phosphoglucomutase 1 deficiency-congenital disorder of glycosylation (PGM1-CDG; previously called GSD XIV), GSD XV, Fanconi-Bickel syndrome (FBS) and phosphoglycerate kinase (PGK) deficiency. Of note, both lactate dehydrogenase subunit A deficiency and FBS are sometimes referred to as GSD XI in the literature. In this Review, GSD XI refers to lactate dehydrogenase subunit A deficiency, and FBS is referred to by eponym.GSDs seem to represent a phenotypic disease continuum. Compelling examples of this continuum include infantile-onset and late-onset Pompe disease and prenatal-onset GSD IV and adult-onset GSD IV, which is also known as adult polyglucosan body disease (APBD). For example, infantile-onset and late-onset Pompe disease have the same mechanism, which is accumulation of glycogen in lysosomes owing to variants in GAA that cause poor function of the GAA enzyme. The severity of disease and clinical manifestations differ between infantile-onset and late-onset disease owing to genotype-phenotype correlation.Owing to the similar disease mechanisms, the differences in severity and presentation reflect a continuum of one disease process. Understanding of the variable expressivity of these rare conditions improved with the identification of more patients with time, increased awareness and improved genetic testing (which...