This paper presents in a first step, a modelling approach to control auxiliaries of a PEM Fuel Cell and the design of control laws. Anode and Cathode compartments are considered to derive the voltage behaviour of the Fuel Cell and to control air and hydrogen flow rate as well as pressure. In a second step, the structure specification of an electrical power train with Fuel Cell for high power transport applications is presented. Two choppers are designed and controlled to deliver the power demand from the Fuel Cell itself and Storage Elements added. This work shows that we can characterise and adjust the system control on an actual operating cycle. (c) 2004 Elsevier Ltd. All rights reserved.