Glycogen content of white and red skeletal muscles, cardiac muscle, and liver was investigated in conditions where changes in plasma levels of non‐esterified fatty acids (NEFA) occur. The experiments were performed in fed and 12 and 48 h‐fasted rats. The animals were also submitted to swimming for 10 and 30 min. Glycogen content was also investigated in both pharmacologically induced low plasma NEFA levels fasted rats and pharmacologically induced high plasma NEFA levels fed rats. The participation of Akt and glycogen synthase kinase‐3 (GSK‐3) in the changes observed was investigated. Plasma levels of NEFA, glucose, and insulin were determined in all conditions. Fasting increased plasma NEFA levels and reduced glycogen content in the liver and skeletal muscles. However, an increase of glycogen content was observed in the heart under this condition. Akt and GSK‐3 phosphorylation was reduced during fasting in the liver and skeletal muscles but it remained unchanged in the heart. Our results suggest that in conditions of increased plasma NEFA levels, changes in insulin‐stimulated phosphorylation of Akt and GSK‐3 and glycogen content vary differently in liver, skeletal muscles, and heart. Akt and GSK‐3 phosphorylation and glycogen content are decreased in liver and skeletal muscles, but in the heart it remain unchanged (Akt and GSK‐3 phosphorylation) or increased (glycogen content) due to consistent increase of plasma NEFA levels. Copyright © 2009 John Wiley & Sons, Ltd.