If process modelling is a well known approach to compute the performances of fuel cell systems, the optimal design of systems where the process configuration is not fixed a priori remains an issue. The goal of the presented methodology for integrating and optimising fuel cell systems is to help in this preliminary design step. The thermo-economic model developed includes three parts : 1) the energy flow model that represent the thermodynamic performances of the chemical and energy conversions in the physical units operation considered in the system ; 2) the model of the heat transfer system that is based on process integration thechniques [1] and 3) an economic module that computes a cost estimation of each of the devices considered in the system. The method uses a superstructure that includes the major options to be considered for the energy conversion in the system. A multi-objective optimisation approach based on evolutionary algorithms is used to extract from the superstructure the most promising configurations and compute for each of them the best operating conditions. The objectives considered are specific cost of electricity production and the system efficiency. The proposed method is generic and may be applied to diffrent types of fuel cell systems. Here, the results of the thermo-economic optimization are given for a PEM (Proton Exchange Membrane) fuel cell system.