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Over decades, persistent organic pollutants (POPs) and trace metals like mercury (Hg) have reached the remotest areas of the world such as Antarctica by atmospheric transport. Once deposited in polar areas, low temperatures, and limited solar radiation lead to long environmental residence times, allowing the toxic substances to accumulate in biota. We investigated the load of polychlorinated biphenyls (PCBs) and dichlorodiphenyltrichloroethane (DDTs) and metabolites (DDEs, DDDs) in embryos from failed eggs of the smallest seabird breeding in Antarctica, the Wilson's storm-petrel (Oceanites oceanicus) at King George Island (Isla 25 de Mayo). We compared samples of different developmental stages collected in 2001, 2003, and 2014 to 2016 to investigate changes in pollutant concentrations over time. We detected eight PCBs including the dioxin-like (dl) congeners PCB 105 and 118 (ΣPCBs: 59-3403 ng g−1 ww) as well as 4,4’-DDE, and 4,4’-DDD (ΣDDX: 19-1035 ng g−1 ww) in the embryos. Samples from the years 2001 and 2003 showed higher concentrations of PCBs than those from 2014 to 2016. Concentrations of DDX was similar in both time intervals. Furthermore, we determined Hg concentrations in egg membranes from 1998 to 2003, and 2014 to 2016. Similar to PCBs, Hg in egg membranes were higher in 1998 than in 2003, and higher in 2003 than in the years 2014 to 2016, suggesting a slow recovery of the pelagic Antarctic environment from the detected legacy pollutants. Embryos showed an increase in pollutant concentrations within the last third of their development. This finding indicates that contaminant concentrations may differ among developmental stages, and it should be taken into account in analyses on toxic impact during embryogenesis.