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A headspace-solid phase microextraction/gas chromatography-mass spectrometry (HS-SPME/GC-MS) method was developed herein for the analysis of virgin olive oil volatile metabolome. Optimisation of SPME conditions was performed by Design of Experiments (DoE) and Response Surface Methodology (RSM) approaches and factors, such as sample volume, sample stirring, extraction temperature and time, and desorption temperature and time, were examined to reach optimal microextraction conditions. The potential of the optimised method was then investigated for its use in the classification of Cretan virgin olive oil samples with the aid of multivariate statistical analysis. Certain markers were identified with significance in the geographical classification of Cretan extra-virgin olive oil (EVOO) samples. In total, 92 volatile organic compounds were tentatively identified and semi-quantified, and the data obtained confirm that the method is robust, reliable, and analytically powerful for olive oil classification.