AbstractMigratory caribou (Rangifer tarandussspp.) is an ecotype of conservation concern that is experiencing increased cumulative stressors associated with rapid climate change and development in Arctic Canada. Increasingly, hair cortisol concentrations (HCCs) are being used to monitor seasonal hypothalamic–pituitary–adrenal axis activity of ungulate populations; yet, the effect of key covariates for caribou (sex, season, sampling source, body location) are largely unknown. The objectives of this research were 4-fold: first, we assessed the impact of body location (neck, rump) sampling sites on HCC; second, we assessed key covariates (sex, sampling method, season) impacting HCCs of caribou; third, we investigated inter-population (Dolphin and Union (DU), Bluenose-East (BNE)) and inter-annual differences in HCC and fourth, we examined the association between HCCs and indices of biting insect activity on the summer range (oestrid index, mosquito index). We examined hair from 407 DU and BNE caribou sampled by harvesters or during capture-collaring operations from 2012 to 2020. Linear mixed-effect models were used to assess the effect of body location on HCC and generalized least squares regression (GLS) models were used to examine the impacts of key covariates, year and herd and indices of biting insect harassment. HCC varied significantly by body location, year, herd and source of samples (harvester vs capture). HCC was higher in samples taken from the neck and in the DU herd compared with the BNE, decreased linearly over time and was higher in captured versus hunted animals (P< 0.05). There was no difference in HCC between sexes, and indices of biting insect harassment in the previous year were not significantly associated with HCC. This study identifies essential covariates impacting the HCC of caribou that must be accounted for in sampling, monitoring and data interpretation.