In this paper, the theoretical analyses are conducted to explore the optimization problems of thermoelectric cooler (TEC) systems applied in electronic cooling. The study mainly focuses on the optimal heat exchanger configuration of a TEC system. The effects of total heat transfer area allocation ratio, thermal conductance of the TEC hot and cold side and TEM element material properties on the cooling performance of the TEC are investigated in detailed based on the developed mathematical model. The analysis results indicate that the highest coefficient of performance (COP), highest heat flux pumping capability of the TEC and lowest cold side temperature can be achieved by selecting an optimal heat transfer area allocation ratio. The optimal heat transfer area allocation ratio mainly depends on the relevant objective functions, the hot and cold side thermal conductance, total heat exchanger size and the TEM element material properties. These results reveal that the heat transfer area allocation ratio is an applicable characteristic of optimum design for TEC systems. It is hoped that the considerations and analysis results may provide guides for the design and application of practical thermoelectric cooler system in electronic cooling. (C) 2013 Elsevier Ltd. All rights reserved.