The multifunctional Ca2+/calmodulin-dependent protein kinase purified from rat brain cytosol undergoes an intramolecular self-phosphorylation or autophosphorylation. Autophosphorylation produces two strikingly different effects on kinase activity that are dependent on the level of ATP used in the reaction. At low but saturating levels of ATP (5 microM), autophosphorylation causes a 75% reduction in kinase activity, with the residual activity still retaining a dependence on Ca2+ and calmodulin. By contrast, at high but physiological levels of ATP (500 microM), the kinase is converted by autophosphorylation to a form that is autonomous of Ca2+ and calmodulin, with no accompanying reduction in activity. The extent of phosphate incorporation does not determine whether the kinase becomes inhibited or autonomous. Autophosphorylated kinase shows the functional change characteristic of the ATP concentration used during the reaction--inhibited at low ATP and autonomous at high ATP--even when compared at the same level of incorporated phosphate. ATP appears to regulate the site(s) phosphorylated during activation of the kinase and thereby modulates the dual effects of autophosphorylation. Events triggered by transient elevations of cellular Ca2+ may be potentiated and retained by generation of the Ca2+/calmodulin-independent protein kinase activity.