Aim: To determine the lipid profile patterns in children with different types of glycogen storage disease (GSD). Methods: The study included 62 children with GSD (43 boys, 19 girls), mean age 8.29 years. All patients underwent anthropometry, assessment of physical development, lipid profile analysis. Results: The children were divided into three groups depending on the type of GSD. Nineteen children (31%) had type I GSD (Group 1), 16 (26%)-type III (Group 2) and 27 (43%)-types VI and IX (Group 3). Dyslipidemia of varying severity was more specific to patients with type I and III GSD. Higher levels of triglycerides were associated with type I GSD, while higher levels of LDL cholesterol were common to type III GSD (P < 0.05) No changes in the lipid profile were observed in 18 (29%): one with type I, 4 with type III, and 13 with types VI and IX. Conclusion: Lipid metabolism disorders were detected in 71% of children with GSD, especially with types I and III. The elevated levels of total cholesterol and LDL cholesterol are associated with the early progression of atherosclerosis and an increased cardiovascular risk in the general population. But there is a lack of evidence of a link between lipid metabolism disorders detected in childhood and an increased risk of cardiovascular diseases in patients with GSDs. More studies needed to investigate this issue.