The aim of this study was to investigate the endothelial dysfunction (ED) and carotid intima-media thickness (IMT) in patients with glycogen storage disease (GSD) types Ia and III. In 22 patients with GSD (13, type Ia; 9, type III) and 18 healthy subjects, endothelial functions of the brachial artery and carotid IMT were evaluated by high-resolution ultrasound. Endothelial-dependent dilatation (EDD) was assessed by establishing reactive hyperemia. EDD and carotid IMTs were compared between the three groups. Mean cholesterol level was slightly higher in GSD type III patients but the difference was not significant. Triglyceride levels and cholesterol to high density lipoprotein (HDL) ratio were significantly higher in GSD type Ia patients. EDD was significantly impaired in GSD type Ia (13% +/- 8%, P = .001) and type III (15% +/- 6%, P = .005) patients when compared with the healthy subjects (22% +/- 4%). The carotid IMT was significantly higher in both GSD type Ia (0.23 +/- 0.03 mm, P =.005) and type III (0.26 +/- 0.05 mm, P = .001) patients when compared with the healthy subjects (0.20 +/- 0.02 mm). Both GSD type Ia and type III patients show significant ED and increased IMT, which are predictors of atherosclerosis.