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In this paper a model of Trailer Refrigeration Units, TRUs, has been developed to quantify the fuel economy and emissions benefits of alternative power systems. Trailer refrigeration units (TRUs) are refrigeration systems typically powered by a separate diesel engine, and they are used to deliver fresh and frozen food products. The products can be very sensitive to temperature variation and maintaining the proper environment is very important. The diesel engines currently used to power the refrigeration system can contribute to high amount of local emissions at the loading warehouse. A promising future alternative is the use of fuel cell auxiliary power units (APUs). In this paper we have developed a MATLAB/Simulink based modeling of TRUs, and we have used the model to quantify the benefits of alternative power systems. The simulation model consists of an unsteady thermal modeling of TRUs that is coupled to the APU.