Polar volatile organic compounds (PVOCs) such as aldehydes and alcohols are byproducts of normal human metabolism and thus are found in blood and exhaled breath. Perturbation of the normal patterns of such metabolites may reflect exposures to environmental stressors, disease state, and human activity. Presented herein is a specific methodology for assaying PVOC biomarkers in exhaled breath condensate (EBC) samples with application to a series of samples from a controlled chamber exposure to dilute diesel exhaust (DE) or to purified air. The collection/analysis method is based on condensation of normal (at rest) exhaled breaths for 10 min (resulting in 1-2 ml of liquid) with subsequent analyte adsorption onto Tenax cartridges followed by thermal desorption and analysis by gas chromatography/mass spectrometry (GC/MS). Analytical data have linearity of response (R(2)>0.98) across a range of 0-160 ng/ml with a detection limit ranging from 0.2 to 7 ng/ml depending on the compound. Statistical analyses of the results of the controlled exposure study indicate that metabolism, as reflected in simple breath-borne oxygenated species, is not affected by exposure to ambient airborne levels of DE. Linear mixed-effects models showed that PVOC biomarker levels are affected by gender and vary significantly among nominally healthy subjects. Differences among PVOCs analyzed in clinic air, purified chamber air, and chamber air containing dilute DE confirm that most of the compounds are likely of endogenous origin as the exogenous exposure levels did not perturb the EBC measurements.