In the last two decades, phenolic compounds occurring in olive oils known as secoiridoids have attracted a great interest for their bioactivity. Four major olive oil secoiridoids, i.e., oleuropein and ligstroside aglycones, oleacin and oleocanthal, were previously characterized in our laboratory using reversed-phase liquid chromatography with electrospray ionization-Fourier transform-mass spectrometry (RPLC-ESI-FTMS). The same analytical approach, followed by multivariate statistical analysis (i.e., Principal Component Analysis), was applied here to a set of 60 Italian extra-virgin olive oils (EVOO). The aim was to assess the secoiridoid contents as a function of olive cultivars, place of cultivation (i.e., different Italian regions) and olive oil processing, in particular two- vs. three-phase horizontal centrifugation. As expected, higher secoiridoid contents were generally found in olive oils produced by two-phase horizontal centrifugation. Moreover, some region/cultivar-related trends were evidenced, as oleuropein and ligstroside aglycones prevailed in olive oils produced in Apulia (Southern Italy), whereas the contents of oleacin and oleocanthal were relatively higher in EVOO produced in Central Italy (Tuscany, Lazio and Umbria). A lower content of all the four secoiridoids was generally found in EVOO produced in Sicily (Southern Italy) due to the intrinsic low abundance of these bioactive compounds in cultivars typical of that region.