The effects of amylin and insulin on the phosphorylation of glycogen synthase and phosphorylase were investigated using rat diaphragms incubated with 32Pi. Muscles were incubated with insulin (200 nM) or amylin (200 nM) for 30 min before extracts were prepared. The 32P contents of the enzymes were determined after immunoprecipitation and SDS-polyacrylamide gel electrophoresis. Amylin increased both the activity ratio (-AMP/+AMP) and the 32P content of phosphorylase by approximately 2-fold. Insulin alone was without significant effect on phosphorylase, but insulin blocked the effect of amylin on increasing the phosphorylation of phosphorylase. Insulin increased the glycogen synthase activity ratio (low glucose-6-P/high glucose-6-P) by approximately 80%. Amylin decreased this ratio from 0.14 to 0.08 and increased the phosphorylation of synthase by approximately 40%. To investigate changes in phosphorylation of different sites in the synthase, the enzyme was subjected to exhaustive proteolysis with trypsin, and 32P-labeled fragments were separated by reverse phase high performance liquid chromatography. Insulin decreased the 32P contents of sites 3(a+b+c) and 2(a+b), which appears to account for the increase in synthase activity. Amylin increased phosphorylation of sites 1a, 1b, and 3(a+b+c), but not sites 2(a+b). With insulin plus amylin, phosphorylation of none of the sites was significantly changed. The results indicate that the effects of amylin on glycogen synthase must involve more than activation of cAMP-dependent protein kinase, as this kinase phosphorylates site 2 and does not phosphorylate sites 3(a+b+c).