The measurement of volatile organic compounds in exhaled breath is becoming recognized as a method of disease diagnosis and therapeutic monitoring. The aim of this study was to validate the collection of breath from intubated patients in the intensive care setting. This was done by assembling a system of ventilators and humidification to emulate the human respiratory system. A known concentration of acetone was spiked into the system to simulate alveolar and dead-space 'breath'. Selected-ion flow tube mass spectrometry (SIFT-MS) was used to directly measure gas at two separate points (headspace, distal circuit end) and from Tedlar bags collected using a remote breath fractionator. The mean acetone concentration for headspace, distal circuit end and Tedlar bag concentrations were calculated. The fractionator was effective in separating the early (dead space) and late phases of exhaled breath. Results from the late Tedlar bag samples collected by the remote breath fractionator showed a clear correlation with headspace and distal circuit end acetone concentrations. The collection for remote analysis of breath samples from immobile patients is made possible using the breath fractionator in conjunction with SIFT-MS analysis.