Purpose: The aim of this study was to characterize the pathogenesis of low bone mineral density in glycogen storage disease type Ia and Ib. Methods: A retrospective chart review performed at the University of Florida Glycogen Storage Disease Program included patients with glycogen storage disease type Ia and Ib for whom dual-energy X-ray absorptiometry analysis was performed. A Z- score less than -2 SD was considered low. Analysis for association of bone mineral density with age, gender, presence of complications, mean triglyceride and 25-hydroxyvitamin D concentrations, erythrocyte sedimentation rate, duration of granulocyte colony-stimulating factor therapy, and history of corticosteroid use was performed. Results: In glycogen storage disease Ia, 23/42 patients (55%) had low bone mineral density. Low bone mineral density was associated with other disease complications (P = 0.02) and lower mean serum 25-hydroxyvitamin D concentration (P = 0.03). There was a nonsignificant trend toward lower mean triglyceride concentration in the normal bone mineral density group (P = 0.1). In patients with glycogen storage disease type Ib, 8/12 (66.7%) had low bone mineral density. We did not detect an association with duration of granulocyte colony-stimulating factor therapy (P = 0.68), mean triglyceride level (P = 0.267), erythrocyte sedimentation rate (P = 0.3), or 25-hydroxyvitamin D (P = 0.63) concentration, and there was no evidence that corticosteroid therapy was associated with lower bone mineral density (P = 1). Conclusion: In glycogen storage disease type Ia, bone mineral density is associated with other complications and 25-hydroxyvitamin D status. In glycogen storage disease type Ib, bone mineral density was not associated with any covariates analyzed, suggesting multifactorial etiology or reflecting a small sample. Genet Med 2012:14(8):737-741