I Email address: mwang(a),lanl.!!ov (M.W.); gkang@lanLgov (Q.K) Electrokinetic tr"t1'~n{',rt In microchannels Abstract: We present a numerical framework to model the electrokinetic transport in microchannels with random roughness. The three-dimensional microstructure of the rough channel is generated by a random generation-growth method with three statistical parameters to control the number density, the total volume fraction and anisotropy characteristics of roughness elements. The governing equations for the electrokinetic transport are solved by a high efficiency lattice Poisson-Boltzmann method in complex geometries. The effects from the geometric characteristics of roughness on the electrokinetic transport in microchannels are therefore modeled and analyzed. For a given total roughness volume fraction, a higher number density leads to a lower fluctuation due to the random factors. The electroosmotic permeability increases with the roughness number density nearly at a logarithmic law for a given volume fraction of roughness, but decreases with the volume fraction of roughness for a given roughness number density. When both the volume fraction and the number density of roughness are given, the electroosmotic permeability is enhanced by increases of the characteristic length along the external electric field direction or decreases of the length of the direction of across the channel.For a given microstructure of rough microchannel, the electroosmotic permeability decreases with the Debye length. Compared with the corresponding flows in a smooth channel, the rough surface may enhance the electrokinetic transport when the Debye length is smaller than the roughness characteristic height under the assumption of constant zeta potential for all surfaces.The present results may improve the understanding of the electrokinetic transport characteristics in microchannels.