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 a significantly 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 2000 were included in the study to provide a reference sea eagle population outside of the Baltic Sea region. The concentrations of ∑PCDD, ∑PCDF and ∑non-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 ∑PCDD/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 T(2) test). We found no significant differences in 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.