Optimization of the Varian Saturn 2200 ion-trap tandem mass spectrometry (IT-MS/MS) system and comparison of its data quality with two other detection methods [electron-capture detection (ECD) and high-resolution mass spectrometry (HRMS)] was pursued by measuring polychlorinated biphenyls (PCBs) levels in fish and shellfish samples. IT-MS/MS methodology provided limits of detection (LOD) comparable to those obtained by ECD but superior specificity for the detection of a selected number of 39 PCB native congeners and 9 (13)C-labelled PCB standards. The method detection limits (MDLs) established for IT-MS/MS ranged between 1.0 and 5.0 pg/g on a wet weight basis while those obtained by ECD and HRMS were 1.0-4.0 pg/g and 0.1-2.0 pg/g, respectively. Overall, the results obtained in the study demonstrate that gas chromatography (GC) combined with IT-MS/MS provide higher data quality than those achievable by GC-ECD. For this particular set of target analytes the specificity achievable with IT-MS/MS was comparable to that obtained by HRMS and both techniques provided comparable data in terms of accuracy and precision.