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Thyroid hormones play an important role in the regulation of growth, development, metabolism, thermoregulation, and migration. Very little information exists on patterns of thyroid hormone concentrations in healthy mysticete whales, as many studies have focused on ill, entangled, or stranded whales, making it difficult to interpret thyroid hormone trends. In this study, we used a unique sample-set of bowhead whale baleen plates to explore the long-term interrelationships between triiodothyronine (T3), the most biologically active thyroid hormone, corticosterone, testosterone, and nitrogen isotope ratios (δ15N) (proxies for stress, reproduction, and diet, respectively) to investigate the role T3 may play in the physiology of healthy cetaceans. Baleen plates were collected between 1998 and 2011 from eight subsistence-harvested male bowhead whales across the Eastern Canadian Arctic. Each baleen plate generated 88–158 serial samples, representing ~11–22 years of life for each individual whale. T3 concentrations ranged from 0.61 to 21.62 ng/g and varied seasonally in just two whales. Most whales showed no correlation between T3 and seasonal fluctuations in testosterone or δ15N, suggesting that variation in T3 is not driven by seasonal shifts in reproductive cycles, consumer trophic level, or migration. However, a strong positive correlation between T3 and corticosterone was observed in every whale, which we hypothesized was due to non-seasonal factors that simultaneously increase metabolic rate and physiological stress. The positive correlation between T3 with corticosterone suggests that in mysticete whales, some stressors may require increased energetic output.