A new approach to the geographical characterisation of virgin olive oils (VOOs) based on the 1H NMR fingerprint of the unsaponifiable matter is presented. The 1H NMR spectra of the unsaponifiable fraction of virgin olive oils from Spain, Italy, Greece, Tunisia, Turkey, and Syria were analysed by several pattern recognition techniques (LDA, PLS-DA, SIMCA, and CART). PLS-DA (PLS-1 approach) obtained the best classification results for all classes. Moreover, 1H NMR spectra of the bulk oil, and its corresponding unsaponifiable fraction, as well as the subfractions of the unsaponifiable fraction (alcohol, sterol, hydrocarbon, and tocopherol fractions) were studied in the search for the markers that multivariate techniques revealed to be related to the geographical origin of olive oils. Additionally, a preliminary study regarding 1H NMR data of the bulk oil and the corresponding unsaponifiable fraction of VOOs suggested that these spectral data contained complementary information for the geographical characterisation of VOOs.