The stoichiometry of H+ ejection by mitochondria during hydrolysis of a small pulse of ATP (the H+/ATP ratio) has been reexamined in the light of our recent observation that the stoichiometry of H+ ejection during mitochondrial electron transport (the H+/site ratio) was previously underestimated. We show that earlier estimates of the H+/ATP ratio in intact mitochondria were based upon an invalid correction for scalar H+ production and describe a modified method for determination of this ratio which utilizes mersalyl or N-ethylmaleimide to prevent complicating transmembrane movements of phosphate and H+. This method gives a value for the H+/ATP ratio of 2.0 without the need for questionable corrections, compared with a value of 3.0 for the H+/site ratio also obtained by pulse methods.A modified version of the chemiosmotic theory is presented, in which 3 H+ are ejected per pair of electrons traversing each energy-conserving site of the respiratory chain. Of these, 2 H+ return to the matrix through the ATPase to form ATP from ADP and phosphate, and 1 H+ returns through the combined action of the phosphate and adenine nucleotide exchange carriers of the inner membrane to allow the energy-requiring influx of Pi and ADP3-and efflux of ATP4-. Thus, up to one-third of the energy input into synthesis of extramitochondrial ATP may be required for transport work. Since other methods suggest that the H+/site significantly exceeds 3.0, an alternative possibility is that 4 H+ are ejected per site, followed by return of 3 H+ through the ATPase and 1 H+ through the operation of the proton-coupled membrane transport systems.The passage of electrons from substrates to oxygen via the respiratory chain can develop an electrochemical gradient of H+ across the inner membrane of intact mitochondria (1-4). The number of H+ equivalents ejected during passage of a pair of electrons through each of the energy-conserving sites is designated the H+/site ratio (5). According to the chemiosmotic theory of oxidative phosphorylation (1-3, 6), the electrochemical H+ gradient so produced may drive H+ back into the mitochondrial matrix through the mitochondrial ATPase, causing coupled synthesis of ATP. The number of H+ equivalents translocated inward per ATP synthesized is the H+/ATP ratio. Since there is no net production or utilization of H+ during oxidative phosphorylation in vivo, the chemiosmotic theory postulates that the H+/site and the H+/ATP ratios are equal.The original measurements of the H+/site ratio by Mitchell and Moyle (7, 8) yielded the value 2.0 (see also ref. 9). Since measurements of the H+/ATP ratio during hydrolysis of added ATP also gave the value 2.0 in both mitochondria (7,(10)(11)(12)(13)(14) and submitochondrial particles (14, 15), the postulated condition of equality (H+/site = H+/ATP) was apparently fulfilled. However, we have recently demonstrated that the original oxygen-pulse experiments of Mitchell and Moyle (7,8) t To whom reprint requests should be addressed. movements were suppressed, H+/site ratios of ...