Concentrations of polychlorinated dibenzo-p-dioxins (PCDD), polychlorinated dibenzofurans (PCDF), and dioxin-like non-ortho-PCBs were measured in white-tailed sea eagle (WTSE) eagle eggs collected along the Swedish coast of the Baltic Sea during the period 1992–2004. The eggs represent two different subpopulations with significantly different nestling brood sizes; the Baltic Proper (BP) with an approximately normal nestling brood size (1.62), and the south Bothnian Sea (sBS) with reduced nestling brood size (1.22) combined with asigni ficantly higher rate of dead eggs. The aim was to investigate if this difference in reproductive outcome was linked to differences in exposure to dioxin-like compounds. Three eggs collected in Greenland in 200 were included in the study to provide a reference sea eagle population outside of the Baltic Sea region. The concentrations of ΣPCDD, ΣPCDF and Σnon-ortho-PCB in the two subpopulations from the Baltic Sea (BS) region ranged from 0.41–4.1, 1.2–5.3 and 180–970 ng/g lipids, respectively, while in the Greenland population the ranges were 0.11–0.16, 0.22–0.33 and 57–83 ng/g lipid, respectively. 2,3,4,7,8-PCDF was the predominant congener in all areas and accounted for on average 31–49% of the total ΣPCDD/F concentrations. The total toxic equivalents (TEQ) in sBS WTSEs were higher (approximately 39 ng TEQ/g lipid) than reported in eggs for many other birds, and the major contributors to the TEQ in the Baltic Sea were the non-ortho-PCBs. A principal component analysis (PCA) showed a difference in congener pattern between the two Baltic regions that was statistically significant (Hotelling's T2 test). Wefound no significant differencesin the total TEQ between the two populations (sBS–BP) and thus no evidence was found linking the reproductive impairment in WTSE in sBS to the concentrations of PCDD/Fs or non-ortho-PCBs in the eggs.