Harbour seals (Phoca vitulina) and harbour porpoises (Phocoena phocoena) are top predators in the North Sea and consequently accumulate a variety of pollutants in their tissues. Concentrations of polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs) and their hydroxylated metabolites (HO-PCBs and HO-PBDEs) were measured in serum of wild harbour seals (n = 47) and captive harbour porpoises (n = 21). Both species exhibit long life spans and do not have extreme situations, such as complete fasting during periods of lactation, in their annual cycles. For PCBs, concentrations in adult males were slightly higher than in juveniles and lowest in juvenile females. For PBDEs, juveniles have higher levels than adult males and females, probably as a consequence of lactational transfer. However, differences between these age-gender groups were not statistical significant, indicating that individual variation was limited within each species, even without knowing the feeding status of the animals. Body condition, particularly emaciation, has a major influence on the levels of chlorinated and brominated contaminants in serum. Profiles of PCBs were CB 153 N CB 138 N CB 187 N CB 180 and CB 153 N CB 138 N CB 149 N CB 187 N CB 180 for harbour seals and porpoises respectively. For PBDEs, BDE 47 was the predominant congener followed by BDE 100 and 99 in both species. In harbour seals, concentrations of sum PCBs (median: 39,200 pg/ml) were more than 200 times higher than levels of sum PBDEs (median: 130 pg/ml) and almost 10 times higher than concentrations of sum HO-PCBs (4350 pg/ml). In harbour porpoises, concentrations of sum PCBs (median: 24,300 pg/ml) were about 20 times higher than concentrations of PBDEs (median: 1300 pg/ml). HO-PCBs were detected in only 4 harbour porpoises and this at very low concentrations. Naturally-produced MeOPBDEs were only found in harbour porpoises at concentrations ranging from 120 to 810 pg/ml. HO-PBDEs were not found in any species. In general, harbour seals accumulate less compounds and have mostly lower concentrations than harbour porpoises possibly as a result of a better developed metabolism.