High quality extra virgin olive oils represent an optimal source of nutraceuticals. The European Union (EU) is the world’s leading olive oil producer, with the Mediterranean region as the main contributor. This makes the EU the greatest exporter and consumer of olive oil in the world. However, small olive oil producers also contribute to olive oil production. Beneficial effects on human health of extra virgin olive oil are well known, and these can be correlated to the presence of vitamin E and phenols. Together with the origin of the olives, extraction technology can influence the chemical composition of extra virgin olive oil. The aim of this study was to investigate the concentration of potentially bioactive compounds in Italian extra virgin olive oils from various sources. For this purpose, vitamin E and phenolic fractions were characterized using high-performance liquid chromatography (HPLC) coupled with fluorescence, photodiode array and mass spectrometry detection in fifty samples of oil pressed at industrial plants and sixty-six samples of oil produced in low-scale mills. Multivariate statistical data analysis was used to determine the applicability of selected phenolic compounds as potential quality indicators of extra virgin olive oils.