Investigators have demonstrated that faecal VOCs are relatively stable over time within and between individuals despite day-to-day variation in diet and are not affected by freezing and storage of stool samples. We have optimized procedures for stool handling for metabolite extraction for gas chromatography-mass spectrometry (GC-MS) analysis (sample volume, solid phase micro-extraction fibre coating, extraction conditions [temperature and time] and vial volume and also developed the advanced statistical methods required for determining and comparing VOC profiles.