A 2-D-HPLC/CE method was developed to separate and characterize more in depth the phenolic fraction of olive oil samples. The method involves the use of semi-preparative. HPLC (C18 column 250 x 10 mm, 5 mu m) as a first dimension of separation to isolate phenolic fractions from commercial extra-virgin olive oils and CE coupled to TOF-MS (CE-TOF-MS) as a second dimension, to analyze the composition of the isolated fractions. Using this method, a large number of compounds were tentatively identified, some of them by first time, based on the information concerning high mass accuracy and the isotopic pattern provided by TOF-MS analyzer together with the chemical knowledge and the behavior of the compounds in HPLC and CE. From these results it can be concluded that 2-D-HPLC-CE-MS provides enough resolving power to separate hundreds of compounds from highly complex samples, such as olive oil. Furthermore, in this paper, the isolated phenolic fractions have been used for two specific applications: quantification of some components of extra-virgin olive oil samples in terms of pure fractions, and in vitro studies of its anti-carcinogenic capacity.