Calcium/calmodulin-dependent protein kinase II (CaM kinase II) is composed of two distinct but related subunits, alpha and beta, in various ratios. To investigate the physiological significance of this variation, we have studied the effect of autophosphorylation of CaM kinase II isoforms purified from forebrain and cerebellum on the activity, and analyzed their endogenous protein substrates. Autophosphorylation of two kinases resulted in the appearance of Ca2(+)-independent activity and the substrate specificity of the Ca2(+)-independent form differed from that of the Ca2(+)-dependent, non-phosphorylated form of the enzyme. Increased phosphorylation of two kinases resulted in a decrease in the enzyme activity. The decrease in the enzyme activity of forebrain CaM kinase II was larger than that of cerebellar kinase. Phosphorylated forms of two kinases were less stable than the non-phosphorylated forms, and the phosphorylated form of forebrain kinase was less stable than that of cerebellar kinase. Many endogenous protein substrates of respective CaM kinase II were found in both soluble and particulate fractions of forebrain and cerebellum using gel electrophoresis. Although the major protein substrates of CaM kinase II were almost the same in forebrain and cerebellum, some of the endogenous protein substrates of respective CaM kinase II were found to be different in both soluble and particulate fractions of forebrain and cerebellum.