Long-term physiological stress in individual animals may be an important mechanism linking ecological change with impaired wildlife population health. In the Southern Hudson Bay (SH) subpopulation of polar bears (Ursus maritimus), increasing stress associated with climate warming may be related to declining body condition. Accordingly, the development of tools to assess long-term stress in this species may prove invaluable for conservation efforts in this threatened population. The measurement of hair cortisol concentration (HCC) has shown promise as a potential biomarker of long-term stress in free-ranging bears. However, to serve as a useful management tool, factors influencing HCC in polar bears must be identified and then revealed to establish linkages between environmental conditions and the fitness of individual animals. We determined HCC (median = 0.48 pg/mg [range = 0.16–2.26 pg/mg]) in 185 polar bears captured in southern Hudson Bay from 2007 to 2009. HCC was influenced by sex, family group status, and capture period but not by body region or hair type. Using models developed through a combination of hypothesis testing and information theory, we also determined that HCC was negatively associated with growth indices (length, mass, and body condition index) linked to fitness in polar bears. Additional research will be required across several polar bear populations to establish the utility of HCC as a tool for polar bear conservation. © 2012 The Wildlife Society.