High resolution thermal infrared imaging is a pioneering method giving indices of sympathetic activity via the contact-free recording of facial tissues (thermal imprints). Compared to established stress markers, the great advantage of this method is its non-invasiveness. The goal of our study was to pilot the use of thermal infrared imaging in the classical setting of human stress research. Thermal imprints were compared to established stress markers (heart rate, heart rate variability, finger temperature, alpha-amylase and cortisol) in 15 participants undergoing anticipation, stress and recovery phases of two laboratory stress tests, the Cold Pressor Test and the Trier Social Stress Test. The majority of the thermal imprints proved to be change-sensitive in both tests. While correlations between the thermal imprints and established stress markers were mostly non-significant, the thermal imprints (but not the established stress makers) did correlate with stress-induced mood changes. Multivariate pattern analysis revealed that in contrast to the established stress markers the thermal imprints could not disambiguate anticipation, stress and recovery phases of both tests. Overall, these results suggest that thermal infrared imaging is a valuable method for the estimation of sympathetic activity in the stress laboratory setting. The use of this non-invasive method may be particularly beneficial for covert recordings, in the study of special populations showing difficulties in complying with the standard instruments of data collection and in the domain of psychophysiological covariance research. Meanwhile, the established stress markers seem to be superior when it comes to the characterization of complex physiological states during the different phases of the stress cycle.