The midgut of the tobacco hornworm (Manduca sexta) is a highly aerobic tissue that is destroyed and replaced by a pupal epithelium at metamorphosis. To determine how oxidative phosphorylation is altered during the programmed death of the larval cells, top-down control analysis was performed on mitochondria isolated from the midguts of larvae before and after the commitment to pupation. Oxygen consumption and protonmotive force (measured as membrane potential in the presence of nigericin) were monitored in order to determine the kinetic responses of the substrate oxidation system, proton leak, and phosphorylation system to changes in the membrane potential. Mitochondria from pre-commitment larvae have higher respiration rates than post-commitment larvae. State 4 respiration is controlled by both the proton leak and the substrate oxidation system. In state 3, the substrate oxidation system exerted 90% of the control over respiration and this high level of control did not change with development. Elasticity analysis, however, revealed that after commitment, the activity of the substrate oxidation system falls. This decline may be due, in part, to a loss of cytochrome c from the mitochondria. There are no differences in the kinetics of the phosphorylation system indicating that neither the F₁F_o ATP synthase nor the adenine nucleotide translocase are affected in the early stages of metamorphosis. An increase in proton conductance was observed in mitochondria isolated from post-commitment larvae, indicating that membrane area, lipid composition, or proton-conducting proteins may be altered during the early stages of the programmed cell death of the larval epithelium.