Environmental exposures, individual activities and disease states can perturb normal metabolic processes and be expressed as a change in the patterns of polar volatile organic compounds (PVOCs) present in biological fluids. We explore the measurement of volatile endogenous biomarkers to infer previous exposures to complex mixtures of environmental stressors. It is difficult to extract such compounds for ultra-trace level analysis due to their high solubility in water, especially when assaying complex liquid biological media such as exhaled breath condensate (EBC). Existing methods tend to be limited in sample volume processed and restricted in sample throughput. We have developed an alternative passive extraction method wherein a 2 ml sample is injected into a 75 ml glass bulb creating a small pool of liquid; a standard Tenax® sampling tube is inserted above the fluid and allowed to equilibrate with the headspace for ~24 h. The biomarker compounds are preferentially transferred by diffusion from the aqueous sample onto the Tenax® adsorbent; blanks and calibration samples are similarly processed. Numerous samples can be simultaneously prepared and stored awaiting routine analysis for a suite of alcohols and aldehydes using thermal desorption gas chromatography–mass spectrometry (GC–MS). We have optimized the procedures and estimated the sensitivity, precision and extraction efficiency resulting from the preparation and analytical procedures using synthetic samples. We subsequently demonstrated the method using anonymous biological specimens of EBC from healthy adults. The ultimate goal is to develop normal ranges and patterns for PVOCs to infer population-based environmental health states with simple spot measurements based on outlier determinations.