Amphibian populations are declining worldwide, and increased exposure to environmental stressors, including global climate change and pathogens like Batrachochytrium dendrobatidis (Bd), may be contributing to this decline. Our goal was to use a novel dermal swabbing method to measure glucocorticoid (GC) hormones and investigate the relationship among disease and environmental conditions in the critically endangered Wyoming toad (Anaxyrus baxteri). Our objectives were to (i) validate the use of dermal swabs to measure GCs using an adrenocorticotropic hormone (ACTH) challenge on eight captive toads (4 ACTH: 2 M, 2F and 4 saline as a control: 2 M, 2F), (ii) investigate stress physiology and disease status of toads across six reintroduction sites and (iii) compare dermal cortisol between reintroduced and captive toads. Dermal cortisol peaked immediately after the ACTH and saline injections. Faecal GC metabolites (FGMs) were significantly higher one week after the ACTH injection compared with the week before. Saline-injected toads had no change in FGM over time. Toads were only found in three reintroduction sites and dermal cortisol was similar across sites; however, reintroduced toads had higher dermal cortisol in August compared with June and compared with captive individuals. Bd status did not influence dermal cortisol concentrations. Dermal and faecal hormonal metabolite analyses can be used to study amphibian stress physiology and learn how environmental conditions are impacting population success.