Chemical analysis of exhaled breath condensate (EBC) is an emerging method to non-invasively identify and measure potential biomarkers of disease. Various EBC collection methods have been proposed, each with strengths and weaknesses. Recent evidence in the literature suggests that sample collection methodologies could introduce potential artifacts in biomarker measurements. In this study, we tested the effect of thermal changes during condensate collection on measured EBC chemical concentrations. Using both actively-cooled and passively-cooled devices, we measured distinct differences in the amount of condensate that can be collected over discrete time periods. We also found that concentrations of acetone varied with the thermal profile changes in the collection devices, in apparently identical EBC samples. Together, this evidence suggests that great care should be taken to standardize EBC collection methods, and that small deviations in the thermal properties of the collection devices could contribute to confounding EBC measurement artifacts. This has implications for the design and development of future portable breath analysis systems, especially miniature hand-held devices.