A series of fatty acids among other compounds have recently been detected in breath in real time by secondary electrospray ionization mass spectrometry (SESI-MS) (Martínez-Lozano P and Fernández de la Mora J 2008 Anal. Chem. 80 8210). Our main aim in this work was to (1) quantify their abundance in breath calibrating the system with standard vapors and (2) extend the study to a control group for several days, both under fasting conditions and after sucrose intake. For the quantitative study, we fed our system with controlled amounts (∼140-1440 ppt) of fatty acid vapors (i.e. propanoic, butanoic, pentanoic and hexanoic acids). As a result, we found sensitivities ranging between 1 and 2.2 cps/ppt. Estimated concentrations of these particular acids in the breath of a fasting subject were in the order of 100 ppt. These values were in reasonable agreement with those expected from reported typical plasma concentrations and Henry constants. A second set of experiments on three fasting individuals before and after ingesting 15 g of sucrose showed that the concentration of propionic and butanoic acids increased rapidly in breath for two subjects. This response was attributed to bacterial activity in mouth and pharynx. In contrast, a third subject showed no response to the administration of sucrose. In addition, we performed a survey among six fasting subjects comparing nasal and mouth exhalations during 11 days, 4 months apart. The signal intensity was comparable for mouth and nose breath. This observation, in conjunction with the quantitative study, suggests that these compounds are mostly systemic when measured under fasting conditions. We finally used the NIST MS search algorithm to evaluate the possibility of recognizing a breathing subject based on his/her breath signature. The global recognition score was 63% (41 out of 65), while the probability by chance alone was 6 × 10(-17). This indicates that (i) there are statistically recognizable differences in individual breath patterns and (ii) the breath pattern for a given subject is relatively stable in time. This is consistent with previous NMR-based studies indicating the existence of stable individual metabolic phenotypes.