The paper deals with a problem of a remote prolonged temperature monitoring of biological objects. It presents an algorithm for automatic analysis and processing of video recording from a thermographic camera. Special attention is paid to the limitation of the method taking into account the possibility of its utilizing in laboratory conditions. The proposed algorithm of video analysis has three looped stages: animal location tracking, detecting specific points in the region of interest, and estimation of temperature in these points. The presented method for measuring temperature of the biological object has the following advantage: it minimizes influence on the object of the interest, and thus allows clearer understanding of animal reaction to medication or treatment.