Polychlorinated naphthalenes (PCNs) and non-ortho chlorinated biphenyls (non-ortho CBs) were analysed in blubber, nuchal fat, liver, muscle, kidney and brain of three male harbour porpoises (Phocoena phocoena) from the west coast of Sweden. To estimate spatial variation, PCNs and non-ortho CBs were analysed in six blubber samples collected at different anatomical sites of each animal. Highest wet weight concentrations of sigma PCNs were detected in the lipid rich tissues (blubber and nuchal fat) and liver (520-730 and 520 pg/g, respectively) and lowest in brain (22 pg/g). TetraCNs were most abundant in muscle, kidney and brain, while the hexaCNs were most abundant in the lipid rich tissues and liver. The highest lipid weight concentration recorded (11 ng/g) was for the hexaCN congeners no. 66/67 in liver. These coeluting hexaCN congeners accounted for 80-100% of total hexaCNs in all tissues examined. Concentrations of sigma non-ortho CBs were highest in lipid rich tissues (220-280 pg/g wet weight). Non-ortho CB no. 77 and 169 constituted between 62-86% and 4.9-9.3%, respectively, of total sigma non-ortho CBs. No major variation of sigma non-ortho CB concentrations was found between the six different blubber sites but higher sigma PCN concentrations (wet weight) were found dorsally at the peduncle. Toxic equivalent concentrations (TEQs) showed that non-ortho CB no. 126 was the main contributor to total TEQs in all tissues, except liver in which hexaCN congener nos. 66/67 contributed to about 50% of total TEQs.