The 2',3'-dialdehyde derivative of ATP was used as an affinity label to inactivate phsosphorylase kinase in either the presence or absence of Ca2+ and Mg2+ ions. Following inactivation, the residual activity of phorphorylase kinase toward various protein substrates was measured and compared with that retained for conversion of phosphorylase b. Three different classes of substrates were distinguished by this analysis. For the first class (glycogen synthase), inactivation proceeded at the same rate as that measured with phosphorylase conversion, regardless of whether the inactivation was carried out in the presence or absence of the metal ions. For the second class of substrates (troponin I and troponin T), inactivation of the kinase in either the presence or absence of the metals was much more rapid with phosphorylase as substrate. Phosphorylation of the third class of substrates (phosphorylase kinase itself and a synthetic tetradecapeptide) was inactivated in parallel with phosphorylase b when modification was performed in the absence of metals; however, inclusion of Ca2+ and Mg2+ ions in the inactivation mixture caused activity toward phosphorylase b to be lost more rapidly than that toward the alternative substrates. Our results are consistent with a model in which glycogen synthase and phosphorylase b are preferentially phosphorylated at one type of catalytic site in phosphorylase kinase and troponin I and troponin T at another.