Fuel cell power systems have witnessed intense development in the recent years as they offer a clean and efficient alternative for power generation in stationary and transportation applications. In this paper, we present an overview of recent work on dynamic modeling and control design for stationary and transportation fuel cell systems including the research at United Technologies Corporation. The use of equation oriented modeling framework for system level dynamic modeling enabled by tools, such as Dymola and gPROMS is described. It is demonstrated that the non-linear system level models readily allow linear model derivation and the application of advanced control analysis and design techniques that provide more insight into the system level dynamic and control issues in fuel cell systems. The dynamic modeling and advanced control design research performed at UTC for a hydrogen fed PEMFC power plant for a bus and a natural gas fed PEMFC power plant for stationary power generation is described. We also identify, for future research, the challenges and opportunities in several areas relating to fuel cell systems ranging from power management and freeze startup to system level modeling, control, diagnostics and hardware-in-the-loop validation of the control system. The emphasis is on polymer electrolyte membrane fuel cell (PEMFC) systems but phosphoric acid fuel cell (PAFC) systems are also briefly discussed. (c) 2006 Elsevier Ltd. All rights reserved.