Management of liver glycogen storage diseases (GSDs) primarily involves maintaining normoglycemia through dietary modifications and regular glucose monitoring. Self-monitoring of blood glucose is typically done 3-6 times per day, and may not sufficiently capture periods of asymptomatic hypoglycemia, particularly during sleep. Continuous glucose monitoring systems (CGMS) provide 24-h continuous glucose data and have been used effectively in diabetes mellitus to monitor metabolic control and optimize treatment. This is a relatively new approach in GSDs with only a handful of studies exploring this modality. In this study we used Dexcom CGMS to study the glycemic profile of 14 pediatric and six adult patients with GSD I, III, and IX. A total of 176 days of CGMS data were available. The CGMS was found to be a reliable tool in monitoring glucose levels and trends at all times of the day with good concordance with finger-stick glucose values. This study revealed that in addition to overnight hypoglycemia, CGMS can uncover previously undetected, subclinical, low glucose levels during daytime hours. Additionally, the CGMS detected daytime and overnight hyperglycemia, an often overlooked concern in liver GSDs. The CGMS with concurrent dietary adjustments made by a metabolic dietitian improved metabolic parameters and stabilized blood glucose levels. The CGMS was found to be a safe, effective, and reliable method for optimizing treatment in patients with GSD I, III, and IX.