This paper presents a novel tool capable of collecting thermal signatures inside a building by using low-cost IR temperature sensors mounted on-board an aerial platform. The proposed system aims to facilitate the detection of heat loss inside buildings, which is a key aspect for improving energy efficiency in large commercial or industrial buildings. Current detection systems usually require manual labor as well as the use of expensive instrumentation. The proposed system on the other hand, relies on the use of a small unmanned aerial vehicle carrying low-cost thermopile IR sensors. Moreover, the system delivers a fast temperature sensing scheme and it provides coverage to inaccessible areas, thus overcoming the limitations of current mobile platforms which use ground robots. Different experiments were carried out in order to assess the behavior of the sensors as well as to validate the full system. Moreover, the hypothesis that thermopile IR sensors can be used to track temperature signature on-the-fly is validated experimentally with the use of the proposed system over different targets.