Electroosmotic flow is widely used as a primary method of species transport in microscale biological and chemical analysis systems commonly referred to as labs-on-a-chip. In these systems, surface electrokinetic heterogeneity can be introduced either intentionally through micromanufacturing technology, such as microcontact printing, or unintentionally through, for example, bioparticle adhesion. In either case it is desirable to examine the influence of these surface heterogeneities on the electroosmotic flow structure. In this paper a numerical model based on a simultaneous solution to the Nernst-Planck, Poisson, and Navier-Stokes equations is used to examine the electroosmotically driven flow through a microchannel exhibiting a periodically repeating patchwise heterogeneous surface pattern. The simulations have revealed a distinct three-dimensional flow structure that, depending on the degree of heterogeneity, varies from a weak circulation perpendicular to the applied electric field to a fully circulatory flow system. In general the induced flow structure is found to penetrate into the bulk flow no deeper than the length scale of the heterogeneous patches. In addition the electrophoritic influence of the applied electric field on the net charge density in the double layer is shown to cause a significant deviation from the traditional Poisson-Boltzmann distribution. The overall effect of this double-layer rearrangement on the flow structure, however, is found to be negligible.