The oxidation of fatty acids, carbohydrates and amino acids can be measured by quantifying the rate of excretion of labelled CO2 following administration of 14C- or 13C-labelled substrates at whole-body and tissue level. However, there is a theoretical need to correct the oxidation rates for the proportion of labelled CO2 that is produced via oxidation but not excreted. Furthermore, depending on the substrate and position of the C label(s), there may also be a need to correct for labelled C from the metabolized substrate that does not appear as CO2, but rather becomes temporarily fixed in other metabolites. The bicarbonate correction factor is used to correct for the labelled CO2 not excreted. Recently, an acetate correction factor has been proposed for the simultaneous correction of CO2 not excreted and label fixed in other metabolites via isotopic exchange reactions, mainly in the tricarboxylic acid cycle. Changes in metabolic rate induced, for example, by feeding, hormonal changes and physical activity, as well as infusion time, have been shown to affect both correction factors. The present paper explains the theoretical and physiological basis of these correction factors and makes recommendations as to how these correction factors should be used in various physiological conditions.