Most recent studies on the physiology of proglycogen and macroglycogen in skeletal muscles have adopted a homogenization-free acid extraction protocol to separate these 2 pools of glycogen. The purposes of this study were to determine (a) whether this protocol is suitable; (b) if the acid-insoluble glycogen fraction corresponds to proglycogen; and (c) if this fraction accounts for most of the changes in muscle glycogen content, irrespective of muscle fiber types. Using the rat as our experimental model, this study shows that when the conditions of acid extraction are optimized, 52% to 64% of glycogen in rat muscles is found as acid-soluble glycogen as opposed to approximately 16% when glycogen is extracted using a homogenization-free extraction protocol. Moreover, there is no evidence that the acid-insoluble glycogen corresponds to proglycogen because gel chromatography of the acid-insoluble and acid-soluble glycogen fractions shows similar elution profiles of high-molecular weight glycogen. Finally, irrespective of muscle fiber types, the acid-soluble glycogen accounts for most of the changes in total muscle glycogen levels during the fasting-to-fed transition, whereas the levels of the acid-insoluble glycogen remain stable or increase marginally. In conclusion, this study shows that the homogenization-free acid extraction of muscle glycogen underestimates the proportion of acid-soluble glycogen and that the findings of the studies that have adopted such an extraction protocol to examine the physiology of acid-insoluble and acid-soluble glycogens require reexamination.