Increasing anthropogenic activities in the marine environment are potential threats to the health of harbor porpoises by causing unnatural continuous stress to the animals. The present study was a first assessment to investigate stress and thyroid hormones of free-ranging and captive harbor porpoises. In addition, hormone levels were measured to compare those with concentrations of polychlorinated biphenyl (PCB) congeners, p,p’-dichlorodiphenyl trichloroethane (DDT), and p,p’-dichlorodiphenyl dichloroethylene (DDE) in the blood of a limited number of animals (10 free-ranging and 7 captive individuals). Samples of seven captive harbor porpoises were taken at the Dolphinarium Harderwijk (the Netherlands) and the Fjord & Bælt Centre in Kerteminde (Denmark). Blood from 29 free-ranging harbor porpoises was collected within the frame of tagging projects on animals accidentally caught in pound nets in Denmark. Median levels of the catecholamines adrenaline, noradrenaline, and dopamine were higher in free-ranging harbor porpoises compared to the captive animals. The median value of adrenocorticotropic hormone (ACTH) for captive animals from the Fjord & Bælt Centre was almost three-fold lower than in the free-ranging harbor porpoises. The median values of T4 were similar in both captive and free-ranging harbor porpoises (9.3 to 10.8. µg/dL). T3 levels of the investigated harbor porpoises varied widely between individuals. No significant correlation between any investigated hormones and investigated organochlorine compounds was observed. The study provides first results on stress hormones other than cortisol. Further investigations are needed to improve the understanding of stress hormones and the influence of anthropogenic stressors on the health of harbor porpoises.