This paper reviews the current state of modelling and optimisation with regard to fuel cell systems design. The existing models for portable, stationary and transportation fuel cell systems are identified and characterised by approach, state, system boundary, spatial dimension and complexity or detail. The different model-based design approaches such as parametric study, single-objective optimisation and multi-objective optimisation performed using fuel cell system models are summarised. A case study on the design of a fuel cell micro-cogeneration plant is presented to illustrate the use of modelling and optimisation in generating different design alternatives that contain trade-offs between competing objectives. Copyright (C) 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.