Impaired mitochondrial function contributes to copper- and cadmium-induced cellular dysfunction. In this study, we used modular kinetic analysis and metabolic control analysis to assess how Cd(2+) and Cu(2+) ions affect the kinetics and control of oxidative phosphorylation in isolated rat liver mitochondria. For the analysis, the system was modularized in two ways: (a) respiratory chain, phosphorylation and proton leak; and (b) coenzyme Q reduction and oxidation, with the membrane potential (Delta psi) and fraction of reduced coenzyme Q as the connecting intermediate, respectively. Modular kinetic analysis results indicate that both Cd(2+) and Cu(2+) ions inhibited the respiratory chain downstream of coenzyme Q. Moreover, Cu(2+), but not Cd(2+) ions stimulated proton leak kinetics at high Delta psi values. Further analysis showed that this difference can be explained by Cu(2+) ion-induced production of reactive oxygen species and membrane lipid peroxidation. In agreement with modular kinetic analysis data, metabolic control analysis showed that Cd(2+) and Cu(2+) ions increased control of the respiratory and phosphorylation flux by the respiratory chain module (mainly because of an increase in the control exerted by cytochrome bc(1) and cytochrome c oxidase), decreased control by the phosphorylation module and increased negative control of the phosphorylation flux by the proton leak module. In summary, we showed that there is a subtle difference in the mode of action of Cd(2+) and Cu(2+) ions on the mitochondrial function, which is related to the ability of Cu(2+) ions to induce reactive oxygen species production and lipid peroxidation.