Marine apex predators, such as the gray seal (Halichoerus grypus), are exposed to high concentrations of organochlorine (OC) compounds via biomagnification in the food web. These lipophilic pollutants are transferred from the female to her offspring during lactation, and there is particular concern for endocrine disruption in the offspring. Herein we examined associations between the blubber concentrations of polychlorinated biphenyls (PCBs), dichlorodiphenyltrichloroethane (DDT) and metabolites, chlordanes, hexachlorocyclohexanes (HCHs) and hexachlorobenzene (HCB), and plasma concentrations of thyroid hormones (thyroxine [T4] and tri-iodothyronine [T3]) in free-ranging, newly weaned gray seal pups from the Baltic Sea and the Norwegian waters of the Atlantic Ocean. Concentrations of total T3 (TT3) and free T3 (FT3) were significantly lower in the polluted seals from the Baltic Sea. Blubber concentrations of the sum of the analyzed PCB congeners (sigmaPCBs) and the sum of the DDT compounds (sigmaDDTs) were correlated negatively with plasma TT3 and FT3 concentrations. The results from this study indicate that OCs may affect levels of thyroid hormones in free-ranging gray seal pups, and that more focus should be put on T3 when addressing the possible effects of OCs on thyroid hormone function and status in nonrodent species.