Phenolic compounds are of fundamental importance to the quality and nutritional properties of virgin olive oils. In this paper, the high-performance liquid chromatographic analysis of simple and complex olive oil phenols in the streams generated in the two-phase extraction system was carried out using Arbequina and Picual olives. The malaxation stage reduced the concentration of orthodiphenols in oil ca. 50-70%, while the concentration of the nonorthodiphenols remained constant, particularly the recently identified lignans 1-acetoxypinoresinol and pinoresinol. Oxidation of orthodiphenols at laboratory scale was avoided by malaxing the paste under a nitrogen atmosphere. Phenolic compounds in the wash water used in the vertical centrifuge were also identified. Hydroxytyrosol, tyrosol, and the dialdehydic form of elenolic acid linked to hydroxytyrosol were the most representative phenols in these waters. Hence, phenolic compounds in the wash waters came from both the aqueous and the lipid phases of the decanter oily must.