Background Late-onset glycogen storage disease type II (GSD II, Pompe disease) is an autosomal recessive disease exhibiting progressive proximal skeletal muscle weakness and respiratory muscle involvement, caused by deficiency of the lysosomal enzyme acid α - glucosidase (GAA). Most of patients died of respiratory failure. Methods Eleven patients with late-onset glycogen storage disease type 11 underwent respiratory function evaluation, whose diagnosis was confirmed by muscle pathology, GAA activity assay and gene analysis. Respiratory function evaluation included upright and supine position of forced vital capacity (FVC), forced expiratory volume at the first second (FEV1), maximal inspiratory pressure (MIP), maximal expiratory pressure (MEP) and cough peak flow (CPF). All data were compared with predicted value. The decreased value between upright and supine position FVC ( Δ FVC) were calculated. The correlation between respiratory function and the age of onset, disease course, motor function, GAA activity were analyzed. Results All of 11 patients with late-onset glycogen storage disease type 11 showed declined respiratory function compared with predicted value. The upright FVC, upright FEV,, Δ FVC, MIP, MEP and CPF declined in 10, 10, 8, 11, 10, and 10 patients, respectively. All patients had normal FEV1/FVC in both upright and supine position. There was no correlation between upright FVC, Δ FVC and the onset age, disease course, motor function, GAA activity statistically. Conclusions Pulmonary dysfunction is common in late - onset glycogen storage disease type II , with restrictive ventilatory impairment more predominant, which is caused by inspiratory muscle weakness. [ABSTRACT FROM AUTHOR]