Long-range atmospheric transport, ocean currents, and rivers transport environmental contaminants, such as perfluoroalkyl substances (PFASs), to the Arctic. Some of these PFASs may reach high concentrations in the upper trophic levels in the arctic food web due to bioaccumulation and biomagnification, and may disrupt physiological processes due to interference with endogenous compounds. In mammals, thyroid hormones are important for several biological processes, especially during the developmental stages, and studies have shown that PFASs may disrupt the thyroid hormone homeostasis. The hooded seal (Cystophora cristata) is a top predator in the arctic marine food web and is therefore susceptible to high exposure to PFASs, and the pups are suspected to be exposed both in utero and via the milk. The present study reports, for the first time, levels of PFASs in hooded seal mother-pup pairs. The aims of the study were to investigate levels and patterns of PFASs in plasma and milk, and to determine if the PFASs are subject to maternal transfer via milk and/or placenta. The study also investigated associations between concentrations of PFASs and levels of free and total thyroid hormones in plasma. PFOS was the most predominant PFAS, and the mean PFOS levels reported herein were 13.4, 30.4 and 1.24 ng/g w.w. for maternal plasma, pup plasma and maternal milk samples, respectively. Levels were within the range of levels reported in similar studies on pinnipeds. PFAS levels were generally higher in plasma than milk, supporting that binding to plasma proteins limits their incorporation into milk. There were higher levels of PFHxS, PFOS, PFDoA, PFUdA and PFTrDA in plasma of pups than mothers, while levels of PFNA and PFDA were higher in mothers than pups. The current study confirmed maternal transfer of PFASs from hooded seal mothers to pups and that this occurs via milk and probably also placenta. In fact, the multivariate analysis implied that placenta could be a more important transfer route than milk. There were different transfer ratios for PFASs with different carbon chain lengths, with the lowest transfer efficiency for the intermediate chained PFASs. There were negative associations between specific PFASs and free thyroid hormone levels in both maternal and pup plasma, and between total thyroid hormones and specific PFASs in mothers. This indicates effects of PFASs on the thyroid hormone homeostasis. Positive correlations were reported for TT3:FT3 and several PFASs in mothers and for TT4:FT4 and PFTrDA in pups. The study of endocrine disruption is complex; it was therefore difficult to draw any conclusions on possible mechanisms or effects of PFAS exposure on thyroid hormones in hooded seals.