► Associations between PCBs and thymic involution in UK harbour porpoises was tested. ► Associations between PCBs and thymic cysts in UK harbour porpoises was tested. ► Thymic involution was associated with nutritional status and sexual maturity. ► PCBs and thymic involution was associated when total PCB>17mg/kg lipid weight. ► Development of thymic cysts appears predominantly age-related. The associations between polychlorinated biphenyls (PCBs) exposure and involution of lymphoid tissue and development of epithelial-lined cysts in the thymus of UK-stranded harbour porpoises (Phocoena phocoena) (n=170) were tested. Percentage of thymic lymphoid tissue (%TLT) was histologically quantified. Multiple regression analyses (n=169) demonstrated significant positive correlation between %TLT and nutritional status (p<0.001) and significant negative association between %TLT and onset of sexual maturity (p<0.001). However, in a subgroup of porpoises with total PCB levels above a proposed threshold of toxicity (>17mg/kg lipid weight) (n=109), the negative association between %TLT (as dependent variable) and summed blubber concentrations of 25 chlorobiphenyl congeners (∑25CBs) remained significant (p<0.01) along with nutritional status (p<0.001) and onset of sexual maturity (p<0.001). These results suggest PCB-induced immuno suppression may be occurring in harbour porpoises in UK waters but only at concentrations that exceed proposed toxicity thresholds for marine mammals. In contrast, development of thymic cysts appears predominantly age-related.