AbstractSelected ion flow tube mass spectrometry (SIFT‐MS) is a new analytical technique for the real‐time quantification of several trace gases simultaneously in air and breath. It relies on chemical ionization of the trace gas molecules in air/breath samples introduced into helium carrier gas using H3O+, NO+, and O precursor ions. Reactions between the precursor ions and trace gas molecules proceed for an accurately defined time, the precursor and product ions being detected and counted by a downstream mass spectrometer, thus effecting quantification. Absolute concentrations of trace gases in single breath exhalation can be determined by SIFT‐MS down to ppb levels, obviating sample collection and calibration. Illustrative examples of SIFT‐MS studies include (i) analysis of gases from combustion engines, animals and their waste, and food; (ii) breath and urinary headspace studies of metabolites, ethanol metabolism, elevated acetone during ovulation, and exogenous compounds; and (iii) urinary infection and the presence of tumors, the influence of dialysis on breath ammonia, acetone, and isoprene, and acetaldehyde released by cancer cells in vitro. Flowing afterglow mass spectrometry (FA‐MS) is briefly described, which allows on‐line quantification of deuterium in breath water vapor. © 2004 Wiley Periodicals, Inc., Mass Spec Rev 24:661–700, 2005