In this study the deformation effect of a gas diffusion layer (GDL) on the pressure drop of a polymer electrolyte fuel cell (PEFC) separator channel has been investigated both numerically and experimentally. Pressure drop is considered as a diagnostic tool to monitor the performance of a PEFC. The deformation of the GDL caused by the compression pressure plays an important role in the performance of a PEFC since it affects the physical properties of the GDL, such as porosity, permeability and the cross sectional area of the gas channel. The flow behavior in the separator channel and GDL of PEFCs has been investigated by using a transient, isothermal and three-dimensional numerical model. To develop the numerical simulation of PEFC, verification experiments and data acquisition of physical parameters were conducted by mechanical measurements. The experimental results showed that estimating the actual flow configuration in the cell, the GDL deformation shape due to clamping by the separator lands has a significant influence. The numerical result shows that together with the deformation shape, the GDL physical parameter variation also needs to be considered in order to predict the actual flow phenomena. Moreover, the results can estimate the physical parameters under deformed condition qualitatively. (C) 2011 Elsevier B.V. All rights reserved.