Selected ion flow tube mass spectrometry, SIFT-MS, has been used to determine the repeatability of the analysis of volatile metabolites within the breath of healthy volunteers, with emphasis on the influence of sampling methodology. Baseline instrument specific coefficients of variability for examined metabolites were as follows: acetone (1%), ammonia (1%), isoprene (2%), propanol (6%), ethanol (7%), acetic acid (7%), and hydrogen cyanide (19%). Metabolite concentration and related product ion count rate were identified as strong determinants of measurement variation. With the exception of ammonia, an orally released metabolite, variability in repeated on-line breath analysis tended to be lower for metabolites of systemic origin. Standardization of sampling technique improved the repeatability of the analysis of selected metabolites. Off-line (bag) alveolar breath sampling, as opposed to mixed (whole) breath sampling, likewise improved the repeatability of the analysis of all metabolites investigated, with the exception of acetic acid. We conclude that SIFT-MS analysis of common volatile metabolites within the breath of healthy volunteers is both reliable and repeatable. For selected metabolites, the finding that repeatability is improved through modification of sampling methodology may have implications in terms of future recommended practices.