Morphological parameters of a 3D binary image of a porous carbon gas diffusion layer (GDL) for polymer electrolyte fuel cells (PEFC) reconstructed using X-ray nano-tomography scanning have been obtained, and influence of small alterations in the threshold value on the simulated flow properties of the reconstructed GDL has been determined. A range of threshold values with 0.4% increments on the greyscale map have been applied and the gas permeability of the binary images have been calculated using a single-phase lattice Botlzmann model (LBM), which is based on the treatment of nineteen velocities in the three dimensional domain (D3Q19). The porosity, degrees of anisotropy and the mean pore radius have been calculated directly from segmented voxel representation. A strong relationship between these parameters and threshold variation has been established. These findings suggest that threshold selection can significantly affect some of the flow properties and may strongly influence the computational simulation of micro and nano-scale flows in a porous structure. (C) 2009 Elsevier Ltd. All rights reserved.