In vitro studies show that some individual minor polar phenolic compounds (MPC) present in virgin olive oil prevent oxidation of human low-density lipoproteins (LDL), but few data are available on the antioxidant effect of whole oil extract. Thus, whole virgin olive extracts were studied to determine whether they maintain the antioxidant activity and whether this last is linked to MPC composition of a single virgin oil. Using HPLC-DAD the MPC content in Taggiasca and Seggianese virgin olive oils was measured. Taggiasca oil was less rich in total MPC (208.5 mg/L) than Seggianese oil (441.9 mg/L). In addition, the major compounds of Taggiasca oil were lignan derivatives, whereas the major compounds in Seggianese oils were secoiridoid derivatives. Moreover, Taggiasca oil was practically free of 5-hydroxytyrosol and 5-hydroxytyrosol derivatives, deacetoxy-oleuropein aglycone and oleuropein aglycone. The antioxidant activity of the oils on human LDL was evaluated by measuring malondialdehyde and conjugate diene generation induced by copper ions. In both tests, the oil extracts dose-dependently reduced malondialdehyde and conjugate diene generation. Moreover, antioxidant potency correlated with total MPC; thus, Seggianese extract was more active. The two oils differed quantitatively and qualitatively, and these differences influenced their biological activities; thus clinical trials focused on studying the effects of olive oils should specify the oils used.