Common eiders nesting in the Baltic Sea are exposed to generally high levels of contaminants including potentially genotoxic polycyclic aromatic hydrocarbons and organochlorines. Blood samples were collected from eiders at eight sites in the Baltic Sea and two sites in the Beaufort Sea. DNA content variation was estimated using the flow cytometric method, and subsequently utilized as a biomarker of genetic damage. We observed no significant differences in genetic damage among populations within either the Baltic or Beaufort Seas. However, eider populations from the Baltic Sea had significantly elevated estimates of genetic damage compared to populations from the Beaufort Sea.