Studying ecosystem processes in the context of carbon cycling and climate change has never been more important. Stable carbon isotope studies of gas exchange within terrestrial ecosystems are commonly undertaken to determine sources and rates of carbon cycling. To this end, septum-capped vials (‘Exetainers’) are often used to store samples of CO2 prior to mass spectrometric analysis. To evaluate the performance of such vials for preserving the isotopic integrity (δ13C) and concentration of stored CO2 we performed a rigorous suite of tests. Septum-capped vials were filled with standard gases of varying CO2 concentrations (∼700 to 4000 ppm), δ13C values (approx. −26.5 to +1.8‰V-PDB) and pressures (33 and 67% above ambient), and analysed after a storage period of between 7 and 28 days. The vials performed well, with the vast majority of both isotope and CO2 concentration results falling within the analytical uncertainty of chamber standard gas values. Although the study supports the use of septum-capped vials for storing samples prior to mass spectrometric analysis, it does highlight the need to ensure that sampling chamber construction is robust (air-tight). Copyright © 2010 John Wiley & Sons, Ltd.