A semi-automated carbon column method was developed for the analysis of the non-ortho substituted PCB congeners (3,4,4'-tri; 3,4,4',5-tetra; 3,3',4,4'-tetra; 3,3',4,4',5-penta; and 3,3',4,4',5,5'-hexachlorobiphenyl) (PCBs 37, 81, 77, 126 and 169). The system consisted of an AX21 carbon/glass fibre column with a programmable pumping and valving system. Precision and accuracy measurements indicated the method was reproducible for concentrations greater than 50 ng/kg. Canadian Arctic ringed seal and whale blubber samples were analysed using this method. Parts-pertrillion levels (ng/kg) of non-ortho PCBs were found in all samples. The non-ortho and mono-ortho PCBs (2,3,3',4,4'-penta; 2,3,4,4',5-penta; 2,3',4,4',5-penta; 2,3,3',4,4',5-hexachlorobiphenyl) (PCBs 105, 114, 118 and 156) were the major contributors to total TCDD equivalents in the whale samples (98% in beluga and narwhal) and contributed greater than 50% in the ringed seal samples.