Abstract The reactions of carbon dioxide, CO 2 , with the precursor ions used for selected ion flow tube mass spectrometry, SIFT‐MS, analyses, viz. H 3 O + , NO + and O , are so slow that the presence of CO 2 in exhaled breath has, until recently, not had to be accounted for in SIFT‐MS analyses of breath. This has, however, to be accounted for in the analysis of acetaldehyde in breath, because an overlap occurs of the monohydrate of protonated acetaldehyde and the weakly bound adduct ion, H 3 O + CO 2 , formed by the slow association reaction of the precursor ion H 3 O + with CO 2 molecules. The understanding of the kinetics of formation and the loss rates of the relevant ions gained from experimentation using the new generation of more sensitive SIFT‐MS instruments now allows accurate quantification of CO 2 in breath using the level of the H 3 O + CO 2 adduct ion. However, this is complicated by the rapid reaction of H 3 O + CO 2 with water vapour molecules, H 2 O, that are in abundance in exhaled breath. Thus, a study has been carried out of the formation of this adduct ion by the slow three‐body association reaction of H 3 O + with CO 2 and its rapid loss in the two‐body reaction with H 2 O molecules. It is seen that the signal level of the H 3 O + CO 2 adduct ion is sensitively dependent on the humidity (H 2 O concentration) of the sample to be analysed and a functional form of this dependence has been obtained. This has resulted in an appropriate extension of the SIFT‐MS software and kinetics library that allows accurate measurement of CO 2 levels in air samples, ranging from very low percentage levels (0.03% typical of tropospheric air) to the 6% level that is about the upper limit in exhaled breath. Thus, the level of CO 2 can be traced through single time exhalation cycles along with that of water vapour, also close to the 6% level, and of trace gas metabolites that are present at only a few parts‐per‐billion. This has added a further dimension to the analysis of major and trace compounds in breath using SIFT‐MS. Copyright © 2009 John Wiley & Sons, Ltd.