Persistent organic pollutants (POPs) are long-range transported to the Arctic via atmospheric and oceanic currents, where they biomagnify to high concentrations in the tissues of apex predators such as polar bears (Ursus maritimus). A major concern of POP exposure is their physiological effects on vital organ-tissues posing a threat to the health and survival of polar bears. Here we examined the relationship between selected POPs and baculum bone mineral density (BMD) in the East Greenland and seven Canadian subpopulations of polar bears. BMD was examined in 471 bacula collected between years 1996–2015 while POP concentrations in adipose tissue were determined in 67–192 of these individuals collected from 1999 to -2015. A geographical comparison showed that baculum BMD was significantly lowest in polar bears from East Greenland (EG) when compared to Gulf of Boothia (GB), Southern Hudson (SH) and Western Hudson (WH) Bay subpopulations (all p < 0.05). The calculation of a T-score osteoporosis index for the EG subpopulation using WH bears as a reference group gave a T-score of −1.44 which indicate risk of osteopenia. Concentrations of ΣPCB₇₄ (polychlorinated biphenyls), ΣDDT₃ (dichlorodiphenyltrichloroethanes), p,p′-DDE (dichlorodiphenyldichloroethylene), ΣHCH₃ (hexachlorohexane) and α-HCH was significantly highest in EG bears while ΣPBDE (polybrominated diphenyl ethers), BDE-47 and BDE-153 was significantly highest in SH bears (all p < 0.04). Statistical analyses of individual baculum BMD vs. POP concentrations showed that BMD was positively correlated with ΣPCB₇₄, CB-153, HCB (hexachlorobenzene), ΣHCH, β-HCH, ClBz (chlorobenzene), ΣPBDE and BDE-153 (all p < 0.03). In conclusion, baculum density was significantly lowest in East Greenland polar bears despite the positive statistical correlations of BMD vs. POPs. Other important factors such as nutritional status, body mass and body condition was not available for the statistical modelling. Since on-going environmental changes are known to affect these, future studies need to incorporate nutritional, endocrine and genetic parameters to further understand how POP exposure may disrupt bone homeostasis and affect baculum BMD across polar bear subpopulations.