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The paper deals with methodology of simulation study devoted to evaluation of reliability of HDS catalyst testing procedure in pilot three phase fixed bed reactor. Hydrodynamic behaviour of test reactor was determined by residence time distribution method. Residence time and Peclet number of axial dispersion of liquid phase were obtained by nonlinear regression of experimental data. Hydrodesulfurization reaction kinetics was evaluated by analysis of concentration data measured in high pressure trickle-bed reactor and autoclave. Simulation of reaction courses were carried out both by pseudohomogeneous model of ODE in Matlab and heterogeneous reactor model of PDE solved by COMSOL Multiphysics. Final results confirm presumption of eliminating influence of hydrodynamics on reaction kinetic results by dilution of catalyst bed by inert fine particles.