Fluctuating asymmetry (FA) as a measure of environmental stress was studied in polar bear (Ursus maritimus) skulls from East Greenland (n = 300, collected 1892–2004) and Svalbard (n = 391, collected 1950–2004). Nine metric traits in skull and lower jaw were measured. FA levels of each trait were compared between sex/age groups (subadults, adult females, adult males), periods (≤ 1960, ≥ 1960), and localities (East Greenland, Svalbard). The period ≤ 1960 was chosen to represent a period prior to the appearance of organohalogen pollution in the Arctic. Results indicated that Svalbard bears generally had a higher level of FA than those of East Greenland. Overall, no substantial evidence of a linkage between FA and organohalogens was found. Instead, indications were of subpopulations with declining levels of FA over time, suggesting the existence of positive population level effects powerful enough to overrule the influence of stress caused by global warming, pollution, and overharvesting.