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Traditional methods for quantifying the internal temperature of marine mammals require handling live animals, which is not practical for free-swimming baleen whales. Developing a less invasive, more repeatable method would significantly improve our understanding of whale health and thermal physiology. Infrared thermography (IRT) devices compatible with remotely piloted aircraft systems (RPAS) have facilitated qualitative assessments of heat signatures from marine mammals at sea, but absolute temperatures derived using this approach are rare. The goal of this study was to develop a precise empirical method for estimating intranasal temperatures of baleen whales using RPAS-based IRT. We conducted controlled field experiments and flights over North Atlantic right whales (Eubalaena glacialis, NARWs) to develop and test the methodology. Two approaches were evaluated to estimate intranasal temperatures from IRT sensor intensities: a three-point empirical line regression calibrated per flight using known-temperature objects and a generalized linear model incorporating environmental variables. Controlled field experiments demonstrated that the former approach had a median bias of −0.6°C (interquartile range: 1.5ºC), while the latter approach had unexplained negative proportional bias with increasing true temperature of the target object. After accounting for bias, the former approach yielded an average intranasal temperature of 26.9 ± 1.7°C for 21 unique NARWs. The anatomy of the mysticete upper respiratory tract and physiological heat conservation strategies may explain why estimates were low compared to internal temperatures measured from baleen whales using other techniques (30–39ºC). Variability within whales was less than ± 2°C, supporting the use of these methods to monitor the health of individuals over time. However, variability among whales was greater (up to 7ºC). Improvements in our understanding of whale physiology and respiratory mechanics and advancements in RPAS-based IRT calibrations could make this technology more reliable for assessing individual body temperatures and monitoring populations in the future. [ABSTRACT FROM AUTHOR]