Pompe disease is a rare lysosomal storage disorder caused by defect in GAA gene. It results in deficiency of acid alpha glucosidase (GAA) and intra-lysosomal accumulation of glycogen in multiple tissues with variable phenotypes. Here we report a patient with late onset Pompe disease who initially presented with progressive lordosis and deformity of scapula. A 13-year-old boy was referred to our hospital due to progressive lordosis. He was born from uneventful pregnancy and showed normal developmental milestones till 9 years old, when parents detected his mild lordotic posture for the first time. He was brought to the local orthopedic clinics regularly and used spinal braces since 11 years of age, but the lordosis have been progressed over time. He showed significant lordotic posture with mild scapular deformity and waddling gait, yet the motor examination revealed symmetric 5/5 proximal and distal strength. There were no abnormalities on other neurological examination, either. The creatinine phosphokinase level was increased to 661 IU/L (reference, 20-270 IU/L) and electromyography indicated short and polyphasic motor unit action potential, which suggested muscular dystrophy. Echocardiography showed normal cardiac function. Muscle biopsy indicated nonspecific fiber size variation only. Southern blot analysis for D4Z4 indicated normal repeat number. We perform the target next generation sequencing and compound heterozygous mutation in GAA, c.T1316A and c.G2238C were found. Additional enzyme study showed decreased acid alpha glucosidase with acarbose activity (7.2 nm/hr/mg protein, normal control 23.3). We also found a few fibers with purple colored vacuole in hematoxylin & eosin and modified gomori trichrome stain on review of muscle pathology, which was consistent finding of Pompe disease. The patient started to receive enzyme replacement therapy and still maintain his motor performance with normal cardiac function. We report a patient with atypical presentation of late onset Pompe disease who was confirmed by next generation sequencing. The case expands the diagnostic utility of next generation sequencing as well as clinical heterogeneity of the disease.