Using of bio-ethanol as a fuel for fuel cells is especially attractive since it is a renewable energy source which can be produced domestically. Bio-ethanol powered fuel cell systems can be used for portable applications as well as for stationary systems, such as cogeneration plants. The main components of the fuel cell-reformer system for hydrogen production from bio-ethanol are reformer and CO-removal reactors, which require particular attention since these are complex parts of the system. The autothermal reforming (ATR) process of bio-ethanol is investigated in order to find the optimum operating conditions of the reformer and CO-removal reactors. The experimental tests were made on a fully automated ATR fuel cell system at the “Fraunhofer ISE”, using bio-ethanol as a fuel. The system consists of ATR, two-stage water-gas-shift reactors and CO-removal step - methanation. It is assumed that the reformate gas is fed into proton exchange membrane fuel cell and therefore after all cleaning steps the CO concentration should not exceed 20 ppm. The influence of steam to carbon ratio and other important parameters on the amount of hydrogen produced, possibilities to minimise carbon formation and the optimal operational conditions were investigated. All parts of the system were tested in various operational conditions by varying steam to carbon ratio from 1 to 3, air to fuel combustion ratio, ATR inlet temperature, temperatures of water-gas-shift reactors etc. The measured data are in good agreement with the simulations made with “ChemCAD” simulation program. The main goal of the work was to achieve the maximum hydrogen content and the minimum CO content in reformate gas, which is fed in the fuel cell by supplying minimum amount of energy to the system. The main parameter, which helps to compare similar systems, is the total system thermal efficiency, which was also estimated in the work.