Analyses have been performed, using on-line selected ion flow tube mass spectrometry (SIFT-MS), of the breath of three healthy volunteers, as exhaled via the mouth and the nose and also of the air in the oral cavity during breath hold, each morning over a period of one month. Nine trace compounds have been quantified and concentration distributions have been constructed. Of these compounds, the levels of acetone, methanol and isoprene are the same in the mouth-exhaled and the nose-exhaled breath; hence, we deduce that these compounds are totally systemic. The levels of ammonia, ethanol and hydrogen cyanide are much lower in the nose-exhaled breath than in the mouth-exhaled breath and highest in the oral cavity, indicating that these compounds are largely generated in the mouth with little being released at the alveolar interface. Using the same ideas, both the low levels of propanol and acetaldehyde in mouth-exhaled breath appear to have both oral and systemic components. Formaldehyde is at levels in mouth- and nose-exhaled breath and the oral cavity that are lower than that of the ambient air and so its origin is difficult to ascertain, but it appears to be partially systemic. These results indicate that serious contamination of alveolar breath exhaled via the mouth can occur and if breath analysis is to be used to diagnose metabolic disease then analyses should be carried out of both mouth- and nose-exhaled breath to identify the major sources of particular trace compounds.