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Mesoporous materials are promising catalysts for production of biofuels. Herein, H-MCM-41 catalysts with different concentrations of the silica Bindzil binder (10–50 wt%) were prepared and characterized using pulsed-field gradient (PFG) NMR in the powder form and as extrudates. Effective diffusion coefficients (De) are measured in all cases. Diffusivities of n-hexadecane were found smaller for extrudates as compared to the powder catalysts. The estimates of diffusive tortuosity were also determined. PFG NMR data showed one major component that reveals diffusion in interconnected meso- and micropores and one other minor component (1–2%) that may correspond to more isolated pores or may represent complex effects of restricted diffusion. Therefore, several approaches including initial slope analysis of spin-echo attenuation curves, two-component fitting and Laplace inversion were used to discuss different aspects of diffusional transport in the studied H-MCM-41 materials. Correlations between De and the amount of Bindzil, the specific surface area, the micropore volume, the particle size, the total acid sites and the Lewis acid sites are discussed.