Mitochondria from rabbit and dog renal cortex were incubated with 1 mM (14)C-weak acid anions in media containing low (10 mM) or high (40 mM) concentrations of bicarbonate and the steady-state accumulation of labeled anion in the matrix was measured. In the absence of an energy source, no concentration of (14)C-anion in the mitochondrial matrix space was present, but the anion concentration was significantly higher at low- than at high-bicarbonate concentration. Addition of an energy source, usually ascorbate plus tetramethyl-p-phenylenediamine, led to increases in matrix space anion levels and to accentuation of the difference in anion uptake between low- and high-bicarbonate media, so that two to four times as much anion was present at low- than at high-bicarbonate concentrations. The anions affected included substrates for which inner membrane carriers are present in mitochondria, such as citrate, alpha-ketoglutarate, malate, and glutamate, as well as substances which diffuse passively across the inner membrane such as acetate and formate. When a nonbicarbonate medium buffered with Hepes was used, pH change did not alter anion uptake although anion concentrations exceeding those in the medium still developed when an energy source was present. The difference in mitochondrial anion accumulation between low- and high-bicarbonate levels diminished with decreasing temperature or with increasing anion concentration in the medium. Estimation of intramitochondrial pH with [(14)C]5,5-dimethyl-oxazolidine-2,4-dione showed that the pH gradient across the inner mitochondrial membrane was significantly greater with 10 than with 40 mM bicarbonate in the medium.A hypothesis is described that relates this effect of pH and bicarbonate on mitochondrial anion accumulation to the very rapid changes in substrate levels in renal cortex, which develop when acute metabolic acidosis or alkalosis is produced in the intact animal. It is suggested that an abrupt fall in systemic pH and bicarbonate is associated with a shift in substrate in renal cortex out of the cytoplasm and into mitochondria, where some of the added substrate is metabolized. Reduction in the size of the cytoplasmic pool of substrate occurs with relatively little accompanying change in the size of the mitochondrial pool, thus causing a net reduction in the total tissue pool. This mechanism accounts for the reduction in tissue levels of many mitochondrial substrates observed acutely in metabolic acidosis. In metabolic alkalosis, reversal of these effects leads to expansion of the cytoplasmic pool, thereby resulting in the rise in tissue levels of substrates which occurs in this condition.