We have assayed carbonic anhydrase activity (carbonate dehydratase, carbonate hydro-lyase, EC 4.2.1.1) and icarbonate permeability in suspensions of broken and intact guinea pig mitochondria by monitoring the disappearance of C16'080. We found significant activity in preparations from liver and skeletal muscle, but not in preparations from heart muscle, brain, and kidney. Intact mitochondria containing carbonic anhydrase produce a two-phase acceleration of the disappearance of the labeled CO2, which indicates that the enzyme is located in a region more accessible to CO2 than to HCOj-. Acetazolamide inhibits the enzyme activity instantly in broken mitochondria but only after a delay in intact mitochondria, indicating that the enzyme is in a region not immediately accessible to the inhibitor. Sonication of mitochondria containing carbonic anhydrase activity releases the enzyme, which remains in the supernatant after sedimentation of the submitochondrial particles. This shows that mitochondrial carbonic anhydrase is in the matrix compartment and not in, or bound to, the inner membrane. The activity of the enzyme increases markedly with increasing pH. The enzyme activity of intact mitochondria is greater than that of the broken mitochondria at the same pH of the suspending fluid, corresponding to an intramitochondrial pH that is 0.2-0.5 unit more alkaline.CO2 plays an important role in mitochondrial metabolism. The enzymes of the tricarboxylic acid cycle that produce CO2 (1) are located within the mitochondrial matrix (2), as are those enzymes that fix CO2 in the pathways of gluconeogenesis and urea production (3, 4). Prior to 1972, the few studies of the interaction of CO2 and HCO% with mitochondria dealt with the permeability of the inner mitochondrial membrane to these two species and with the possible existence of a mitochondrial carbonic anhydrase. Chappell and Crofts (5) showed that the inner mitochondrial membrane was essentially impermeable to HC0% but readily permeable to C02, a finding now widely accepted (6). Early reports of mitochondrial carbonic anhydrase (7-9) were cautious because of the problem of contamination, with the exception of that of Karler and Woodbury (10). Rossi (11) found 4% of the carbonic anhydrase of rat liver homogenate in the mitochondrial fraction and showed that it was an intramitochondrial enzyme. Mitochondria incubated with 10 ,gM acetazolamide showed no activity. Holton (12) found carbonic anhydrase activity in isolated rat liver mitochondria with both penetrant CO2 and nonpenetrant HCO as substrates. In contrast to these two positive findings with liver mitochondria, Deprez and Francois (13) found no carbonic anhydrase activity in mitochondrial preparations from various tissues, including liver. In all the above studies, carbonic anhydrase activity was measured by change in pH.A functional role for C02/HC0% in providing a counteranion for energy-linked mitochondrial Ca2+ uptake was proposed by Elder (14). Elder and Lehninger (15,16) showed that HCO3 as such cannot se...