Phenolic compounds are useful markers to control olive oil technological processes, including the virgin olive oil (VOO)/water separation after olive oil extraction. In this investigation, VOO extracted from olives of cv. Coratina using a mild oil/water separator called the hydrocyclone sedimentation system (Hydroil) was compared with VOO obtained using a conventional vertical centrifuge separator (Cenoil), which is mostly used in the modern olive oil industry. Secoiridoid aglycones were selected, among phenolic compounds, as markers and analyzed using reversed-phase liquid chromatography coupled to linear quadrupole ion-trap mass spectrometry with electrospray ionization in the negative mode. VOO samples obtained using the Hydroil system were found to contain significantly higher levels of secoiridoid aglycones, compared to the Cenoyl-type samples. In particular, the total content of the aglycones of decarboxymethyl oleuropein, decarboxymethyl ligstroside, ligstroside, and oleuropein, expressed in terms of oleuropein, was estimated as 35.40 AE 0.80 mg kg −1 , compared to 8.06 AE 0.41 mg kg −1 in the Cenoil samples (n = 3). Since no significant difference in residual water (P < 0.05) was found between the two types of VOO samples, the higher amount of secoiridoids obtained for Hydroil-type ones was explained by the lower extent of oxidation occurring during the mild oil/water separation achieved using the Hydroil system. Keywords Secoiridoids Á Virgin olive oil Á Hydrocyclone Á Liquid chromatography Á Mass spectrometry J Am Oil Chem Soc (2018) 95: 665-671. J Am Oil Chem Soc (2018) 95: 665-671 Fig. 4 Pie charts illustrating the percentage composition of secoiridoids semiquantified in control, Hydroil, and Cenoil samples, based on average concentration values reported in Table 2. The nominal m/z values reported in the legend correspond to the following secoiridoid aglycones: m/z 319, DCO; m/z 303, DCL; m/z 377, oleuropein aglycone; and m/z 361, ligstroside aglycone 670 J Am Oil Chem Soc J Am Oil Chem Soc (2018) 95: 665-671