The results of the study of thermal processes in the thermoelectric system for short-term storage and transportation of biological materials are given. The heat and the mathematical model of the system are given. The mathematical description of thermal processes in a device is based on a system of two-dimensional unsteady heat conduction equations with complex boundary conditions. The calculations have been made according to the required modes of biological material short-term storage: temperature range is from –10 to –40 оС, maximum storage time is up to 24 hours; one should be able to warm up the biological material quickly if necessary. Results are presented as a two-dimensional temperature distribution systems with biological material as well as one-dimensional diagrams of temperature changes at different points of the device in time at various values of thermoelectric cooling battery refrigerating capacity.