Comprehensive two-dimensional gas chromatography (GC x GC) with micro electron-capture detection (microECD) has been optimised for the separation of polychlorinated biphenyl congeners with emphasis on the separation of 12 toxic non- and mono-ortho chlorinated biphenyls (CBs), viz. CBs 77, 81, 105, 114, 118, 123, 126, 156, 157, 167, 169 and 189. The selection of the first- and second-dimension columns and the temperature programme optimisation were carried out with a mixture of 90 CBs and the results are compared with those of one-dimensional GC. A complete separation of all 12 priority CBs was obtained with two column combinations, HP-1-HT-8 and HP-1-SupelcoWax-10. With the HP-1-HT-8 column set, ordered structures show up in the two-dimensional plane, with the number of chlorine substituents and their position (ortho vs. non-ortho) being the main parameters of interest. This can help with congener identification. Estimated detection limits are excellent, i.e. about 10 fg. To illustrate the potential and the versatility of GC x GC-microECD, a cod liver extract and a standard mixture of the 17 most toxic polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans together with 90 CBs were analysed as an application.