In the present longitudinal study, we followed volatile organic compounds (VOCs) excreted in exhaled breath of 20 healthy individuals over time, while adhering to a gluten-free diet for 4 weeks prior to adherence to a normal diet. We used gas chromatography coupled with mass spectrometry (TD-GC-tof-MS) in combination with chemometric analysis to detect an array of VOCs in exhaled breath. Multivariate analysis was applied to extract the maximal information from the obtained data. Dietary intake was assessed to verify adherence to the diet and to get insight into macronutrient intake during the intervention period. A set of 12 volatile compounds distinguished the samples obtained during the gluten-free diet from those obtained during a normal diet. Seven compounds could be chemically identified (2-butanol, octane, 2-propyl-1pentanol, nonanal, dihydro-4-methyl-2(3H)-furanone, nonanoic acid and dodecanal) and speculated on a possible origin. Our findings suggest that a gluten-free dietary period had a reversible impact on participants' excreted metabolites visible in their breath. Several explanations are proposed of influencing metabolic status through dietary interventions. Although the exact origin of the discriminating compounds is not yet known, the main goal of this paper was to share a new potential use of exhaled air analysis and might become a useful tool in fields of nutrition and metabolism.