Bioaccumulation of immunosuppressive organochlorines like polychlorinated biphenyls (PCBs) may pose a threat to the health and viability of cetacean populations. To investigate possible associations between chronic exposure to PCBs and infectious disease mortality in harbour porpoises Phocoena phocoena in UK waters, blubber concentrations of 25 individual chlorobiphenyl (CB) congeners in 34 healthy harbour porpoises that died due to physical trauma (mainly by-catch) were compared with CB concentrations in 33 animals that died due to infectious disease. The infectious disease group had significantly greater total 25 CBs (Σ25CBs) concentrations than the physical trauma group (P<0.001). The mean Σ25CBs concentration in animals that died due to physical trauma was 13.6 mg kg−1 extractable lipid whereas the mean concentration in the infectious disease group was 31.1 mg kg−1 extractable lipid. The relationship between higher Σ25CBs and the infectious disease group was not confounded by age, sex, nutritional status, season, location or year of stranding. In addition, adult females had significantly lower Σ25CBs levels than adult males (P<0.05) due to maternal transfer of CBs to offspring. These findings are consistent with the hypothesis that chronic PCB exposure predisposes harbour porpoises in UK waters to infectious disease mortality, although further research is required to test these associations more robustly.