A high-performance liquid chromatography (HPLC) method using a column of 2-(1-pyrenyl) ethyldimethylsilylated silica was developed in this work in order to achieve satisfactory and reproducible fractionation of polychlorinated biphenyls (PCBs) from brominated flame retardants (BFRs) (polybrominated diphenylethers, PBDEs; and polybrominated biphenyls, PBBs). After the study of different chromatographic parameters (mobile phase composition and separation temperature were the most important) an isocratic elution with isooctane:toluene (98:2, v/v) at a flow-rate of 1 mL/min, a temperature of 45• C, and UV-detection at 225 nm was selected for fractionation of PCBs (time region, 4.0-5.8 min) from PBDEs (5.8-9.0 min) and from PBBs (5.8-11.0 min). The applicability of this method to food samples was demonstrated by fractionating PCBs from PBDEs in three food samples (cheese, milk, and fish). Interferences from PCBs (present in real samples at much higher concentrations than PBDEs) were removed in this way. In addition, by analysing these samples by gas chromatography-mass spectrometry (GC-MS) with and without previous fractionation we were able to observe an improvement in detection sensitivity for PBDEs after HPLC fractionation.