Liver and skeletal muscle glycogen metabolism were investigated in rats 1 and 4 weeks after bile duct ligation (BDL) and in pair-fed, sham- operated control rats. Livers were subjected to morphometric analysis to express glycogen content and enzyme activities per mL hepatocytes. One week after BDL, the hepatic glycogen content was 28.8 ± 13.8 versus 38.6 ± 16.4 mg/mL hepatocyte in BDL and control rats, respectively. Total activity of glycogen synthase (50.2 ± 7.0 vs. 63.5 ± 9.4 mU/mL hepatocytes) and glycogen phosphorylase (59.4 ± 12.9 vs. 90.8 ± 18.9 U/mL) were significantly reduced in BDL whereas the active fraction of glycogen synthase (27 ± 6 vs. 38 ± 5%) but not of glycogen phosphorylase was reduced. The skeletal muscle glycogen content was not different between BDL and control rats. Four weeks after BDL, hepatic glycogen content was further reduced (20.5 ± 14.2 vs. 52.9 ± 6.4 mg/mL). Total activity of glycogen synthase (38.8 ± 12.1 vs. 60.1 ± 4.6 mU/mL hepatocytes) and glycogen phosphorylase (127 ± 19 vs. 178 ± 33 U/mL hepatocytes) were both reduced in BDL rats as were their corresponding active fractions (30 ± 18 vs. 66 ± 8% and 58 ± 10 vs. 76 ± 10). At this time point, the glycogen content in soleus muscle was decreased by 64% in BDL. The glucagon plasma concentration was increased in BDL rats at both time points. There were positive correlations between the volume fraction and both hepatic glycogen content and total activity of hepatic glycogen synthase. Plasma glucagon and the active fraction of hepatic glycogen synthase were negatively correlated. The current studies show a progressive decrease in the hepatic and skeletal muscle glycogen content in BDL rats. The observed decrease in the activities of glycogen synthase and phosphorylase suggest that reduced glycogen synthesis is the major mechanism leading to the reduction in the hepatic glycogen content in BDL rats.