Polychlorinated biphenyls (PCBs) are a group of 209 persistent and bio-accumulative toxic pollutants present as complex mixtures in human and animal tissues. Harbor porpoises accumulate some of the highest levels of PCBs because they are long-lived mammals that feed at a high trophic level. Studies typically use the sum of a suite of individual chlorobiphenyl congeners (CBs) to investigate PCBs in wildlife. However, toxic effects and thresholds of CB congeners differ, therefore population health risks of exposure may be under or over-estimated dependent on the congener profiles present. In this study, we found congener profiles varied with age, sex and location, particularly between adult females and juveniles. We found that adult females had the highest proportions of octa-chlorinated congeners whilst juveniles had the highest proportions of tri- and tetra-chlorinated congeners. This is likely to be a consequence of pollutant offloading between mothers and calves during lactation. Analysis of the individual congener toxicities found that juveniles were exposed to a more neurotoxic CB mixture at a time when they were most vulnerable to its effects. These findings are an important contribution towards our understanding of variation in congener profiles and the potential effects and threats of PCB exposure in cetaceans.