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In a joint effort between United Technologies Research Center and the business unit UTC Fuel Cells system level dynamic models are developed and deployed for the design and analysis of fuel cell based power systems. The article describes the scope and challenges within this effort as well as some of the methods and tools used. System level modeling of fuel cell systems is a challenge that few modeling tools can handle due to the heterogeneous nature of the system. The joint work has resulted in a set of proprietary model libraries for unique component designs, building upon publicly and commercially available model libraries and tools. The model libraries have been used to build system models in both stationary and automotive applications. Examples of models that show the model complexity and some simulation results are given in the paper. Since the system models contain a large number of components, the number of the variables for a full system model usually exceeds 500. Simulation of large, complex systems pose special problems not seen when working with smaller models and really stretch the capabilities of the simulation tools. The paper also discuss some lessons learned in this respect.