A kinetic analysis of the decarboxylation of malonyl-CoA and the condensation--CO2 exchange reaction of fatty acid synthesis has been carried out. The analysis supported by experimental evidence defines conditions under which the decarboxylation of malonyl-CoA quantitatively reflects the activity for the condensation reaction between enzyme-bound acyl and malonyl groups. NADP+ decreases the release of 14CO2 from radiolabeled malonyl-CoA by lowering the rates of the processes leading to the formation of triacetic acid lactone. For accurate measurements, the enzyme concentration should be less than 200 micrograms/mL, and malonyl-CoA/enzyme ratios should be 200 or less. Short reaction periods (1 min or less) and inclusion of NADP+ (100 microM) enhance the accuracy of measurements. These analyses have been used to explain the mechanism of malonyl-CoA mediated inactivation of chicken liver fatty acid synthetase and are appropriate for determining the functional condensing site of the polyfunctional polypeptide chains comprising the dimeric enzyme.