A generalized, cell layer scale proton exchange membrane fuel cell (PEMFC) stack dynamic model is presented using VHDL-AMS (IEEE standard Very High Speed Integrated Circuit Hardware Description Language-Analog and Mixed-Signal Extensions) modeling language. A PEMFC stack system is a complex energy conversion system that covers three main energy domains: electrical, fluidic and thermal. The first part of this work shows the performance and the advantages of VHDL-AMS language when modeling such a complex system. Then, using the VHDL-AMS modeling standards, an electrical domain model, a fluidic domain model and a thermal domain model of the PEMFC stack are coupled and presented together. Thus, a complete coupled multi-domain fuel cell stack I-D dynamic model is given. The simulation results are then compared with a Ballard 1.2 kW NEXA fuel cell system, and show a great agreement between the simulation and experimentation. This complex multi-domain VHDL-AMS stack model can be used for a model based control design or a Hardware-in-the-Loop application. (C) 2009 International Association for Hydrogen Energy. Published by Elsevier Ltd. All rights reserved.