Measuring changes in surface body temperature (specifically in eye-region) in vertebrates using infrared thermography is increasingly applied for detection of the stress reaction. Here we investigated the relationship between the eye-region temperature (TEYE; measured with infrared thermography), the corticosterone level in blood (CORT; stress indicator in birds), and some covariates (ambient temperature, humidity, and sex/body size) in a High-Arctic seabird, the Little Auk Alle alle. The birds responded to the capture-restrain protocol (blood sampling at the moment of capturing, and after 30 min of restrain) by a significant TEYE and CORT increase. However, the strength of the TEYE and CORT response to acute stress were not correlated. It confirms the results of a recent study on other species and all together indicates that infrared thermography is a useful, non-invasive measure of hypothalamic-pituitary-adrenal (HPA) axis reactivity under acute activation, but it might not be a suitable proxy for natural variation of circulating glucocorticoid levels.