Tedlar™ bags are a promising medium for remote breath collection and later analysis using SIFT-MS for disease diagnosis. It is important to understand the changes in integrity of samples stored in Tedlar™ bags. However, there is little work into this problem completed to date, and thus little known about these issues. Therefore, a study into the integrity of samples stored in Tedlar™ bags and analysed using SIFT-MS was undertaken. The sample integrity of ammonia, acetone, ethanol, isoprene and pentane, all initially at 3ppm in breath and nitrogen substrates, and stored in Tedlar™ bags was investigated. Experiments tested the effect of storage size (0.5, 1, 3L), storage time (6-48 hours), storage temperature (23℃ - 25℃, 37℃), humidity (0.4 - 4.5% absolute) and inter-bag variation using triplicate bags. The SIFT-MS instrument used was LDI2 located at Christchurch Hospital. The repeatability and precision of LDI2 was established using prepared cylinder samples (0.05% absolute humidity) of acetone, pentane and ethanol tested at seven times over a 250 min time period. A generalised Cauchy distribution was used to give a combined distribution from multiple bags for the sample humidity and compound concentration. A combined measure of the repeatability and precision, T s , ranged between 217 - 349 ppb for ethanol, acetone and pentane. The factors affecting the repeatability and precision were both machine and compound dependant. The effect of the factors differed over time, with different precursors and compounds. No obvious effects of bag storage size on the sample integrity of pentane, isoprene, ethanol and acetone were observed. The absolute humidity change within bag samples was linked to the volume to surface area ratio because it was more affected by permeation and condensation. All compounds in the nitrogen substrate (except for 37℃ stored acetone (NO+)) displayed decreases in sample integrity with time. All compounds in the breath substrate displayed regular losses of sample integrity, except for the 37℃ and 23℃ - 25℃ stored ethanol (NO+) and 37℃ stored ethanol (H3O+), pentane (O2+) and ammonia (H3O+, O2+). The average change of sample integrity for pentane, isoprene, ethanol and acetone ranged from 0.2 to 3.6 times the maximum T s , while ammonia ranged from 0.9 - 10 times. All observed behaviour was reproducible. Absolute humidity and storage temperature affected the sample integrity of acetone, ethanol and ammonia. Generally, the intra-bag variance was comparable between all storage temperatures and substrates while the inter-bag variation was affected by the absolute humidity. Only the initial and final concentrations between precursors for the 23℃ - 25℃ stored breath and nitrogen substrates agreed. The breath substrate samples gave erroneous values for ammonia. Permeation of compounds into the bags from the atmosphere was not significant. The overall issues surrounding storing breath in Tedlar™ bags for analysis using SIFTMS is not the loss of sample integrity, but the kinetics, precision and repeatability of the SIFT-MS instrument. The current kinetics are not adequate to accurately monitor acetone, isoprene, pentane, ammonia and ethanol in breath and stored in Tedlar™ bags at breath absolute humidity levels greater than 3%. Generally, the loss of sample integrity was only marginally outside the repeatability and precision of the machine.