The aim of this paper is to propose a new non-invasive methodology to estimate thermogenesis in newborns with perinatal asphyxia (PA) undergoing therapeutic hypothermia (TH). Metabolic heat production (with respect to either a neonate's body mass or its body surface) is calculated from the newborn's heat balance, estimating all remaining terms of this heat balance utilising results of only non-invasive thermal measurements. The measurement devices work with standard equipment used for therapeutic hypothermia and are equipped with the Global System for Mobile Communications (GSM), which allows one to record and monitor the course of the therapy remotely (using an internet browser) without disturbing the medical personnel. This methodology allows one to estimate thermogenesis in newborns with perinatal asphyxia undergoing therapeutic hypothermia. It also offers information about instantaneous values of the rate of cooling together with values of remaining rates of heat transfer. It also shows the trend of any changes, which are recorded during treatment. Having information about all components of the heat balance one is able to facilitate comparison of results obtained for different patients, in whom these components may differ. The proposed method can be a new tool for measuring heat balance with the possibility of offering better predictions regarding short-term neurologic outcomes and tailored management in newborns treated by TH.