The objective of this paper is to conceptually design a fuel processor system for a 5 kW proton electrolyte membrane fuel cell (PEMFC) system for mobile and portable application. The first section describes the auto-thermal reformer (ATR) system while the second section demonstrates the significance of the water gas shift (WGS) reaction in the system. Shortcut design methods are used for the process units and the characterization curve for each unit is also presented. Kinetic parameters for steam reforming and WGS reactions are also shown. The 5 kW PEMFC requires about 0.08 m(3)/min (3.74 mol/min) of H-2 fuel at the fuel cell stack. The primary fuel source to the ATR system is methanol 0.1 m(3) /min (4 mol/min), which is fed together with steam and oxygen with the ratio of S/C and O-2/C at 1.3:1 and 1:4, respectively. The conceptual design indicates that if the mole ratio of O-2/C is 0.20-0.25, then the hydrogen selectivity is around 2.5-2.6 for complete methanol. Steam is fed at excess condition in both units, ATR and WGS, to avoid reverse WGS reaction. The conceptual design also proved the significance of WGS reaction in the reduction of CO produced in the ATR and indicated the importance of pressure to reduce the bulk size of WGS reactor. Finally from the overall mass balance for fuel processor unit, the ATR product contains H-2: 73%, CO: 2%, and CO2: 25%. The CO level is then further reduced to less than 2000 ppm after the WGS reactor. In addition, this paper also studied the performance of preferential oxidation (PROX) in removing the CO and it was observed that the PROX could reduce the CO to less than 100ppm and performed better than WGS reaction in terms of water management. However, the main problem with PROX is to decide a good catalyst that can give a good selectivity for CO oxidation rather than water formation. (C) 2004 Elsevier B.V. All rights reserved.