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McArdle disease (muscle glycogen phosphorylase deficiency) is a genetic condition associated with exercise intolerance, but how it affects lean mass (LM) and bone mineral content (BMC) and density (BMD) in patients is unknown. We compared these variables between McArdle patients and age-/sex-matched healthy controls and assessed their potential association with physical activity levels in patients.A case–control, cross-sectional design was used to examine LM, BMC, and BMD by using dual-energy x-ray absorptiometry in 136 young adults of both sexes (36 McArdle patients (33 ± 15 yr) and 103 controls (34 ± 11 yr)). Physical activity was assessed using the International Physical Activity Questionnaire.McArdle patients had significantly lower LM values in whole-body and regional sites compared with their corresponding controls, whereas no differences were found (except for the trunk) when physically active patients (n = 23) were compared with controls. All bone-related variables were significantly lower in patients than in controls (average difference of 13% for BMC and 7.6% for BMD). By contrast, no significant differences at the lumbar spine, pelvis, and femur sites were found between physically active patients and controls.We report on a previously undescribed condition in McArdle patients, poor bone health, which warrants further attention because it can occur in relatively young adults. An active lifestyle can at least partly alleviate this disorder presumably because of its beneficial effect on LM.