Consumers demand for portable audio/video/ICT devices has driven the development of advanced power technologies in recent years. Fuel cells are a clean technology with low emissions levels, able to work with renewable fuels and capable, in a next future, to replace conventional power systems meeting the targets of the Kyoto Protocol for a society based on sustainable energy systems. Within such a perspective, the objective of the European project MOREPOWER (Compact direct methanol fuel cells for portable applications) is to develop a low cost, low temperature, portable Direct Methanol Fuel Cell (DMFC; nominal power 250 W) of compact construction and modular design for the potential market area of weather stations, medical devices, signal units, gas sensors and security cameras. This investigation is focused on a conceptual study of the DMFC system carried out in the Matlab/Simulink platform. Two different DMFC configurations were devised in which alternative components arrangements along the methanol recycle line are considered. Based on a number of simulations, the system configuration characterized by a gas-liquid separator for carbon dioxide removal placed upstream the radiator for heat removal shows the most promising results, thanks to an easier design and operability of the radiator itself.