Introduction Glycogen storage disease III (GSD III) is an inborn error of carbohydrate metabolism that involves mainly the liver and skeletal muscles with rare potential systemic complications as osteoporosis. The aim of work of the current study was to screen children with GSD III for osteoporosis using Dual-emission-X-ray absorptiometry (DXA) scan and to measure associated parathormone (PTH) and vitamin D. Our secondary objective is to correlate between the degree of osteoporosis and the muscle state as well as the metabolic control. Material and methods This cross sectional study included 25 GSD III pediatric cases. The liver biochemical profile, creatine kinase (CK), vitamin D2, PTH levels were tested in addition to electromyogram (EMG), echocardiography and DXA. Twenty-five age and sex matched normal healthy controls were subjected to vitamin D2 analysis and compared to cases. Results The mean ±SD age of the patients was 10.52 ± 3.1 years ranging between 5-18 years. Twenty-one patients (84%) had elevated CK levels, 14 patients (56%) had myopathy and three (12%) had sensory polyneuropathy and almost half of the patients had a mild degree of cardiac muscle hypertrophy. Ten patients (40%) had elevated PTH levels. Twenty-one patients (84%) and 96% of the controls had vitamin D2 deficiency. Thirteen patients (52%) had low BMD; two of them had osteoporosis. Patients with high CK levels significantly had low BMD (P= 0.04). Conclusions Pediatric GSD III patients have a significant prevalence of developing low BMD. It is strongly associated with myopathic changes but not significantly related to metabolic control.