The control of the EOF direction and magnitude remains one of the more challenging issues for the optimization of separations in CE. In this work, we investigated the possibility to use non-uniform surface charge distribution for the modulation of the EOF in CE. Non-uniform zeta potentials were obtained by modifying a section of the capillary surface using adsorption of polyelectrolytes. Three different methods were studied: (i) partial polycation coating on a fused silica capillary, (ii) partial polycation (or polyanion) coating on polyelectrolyte multilayers, and (iii) partial polycation coating on a capillary previously modified with poly(ethylene oxide). The magnitude and the direction of the EOF as a function of the coated capillary length were first studied. The stability of the EOF and the separation performances were also considered taking two dialanine diastereoisomers as model compounds. In partially coated capillaries, the average solvent flow is the sum of two contributions: a non-dispersive electroosmotic contribution related to the capillary surface charge, and a dispersive hydrodynamic contribution that depends on the difference of surface charge between the coated and the non-coated capillary zones. To get a better insight into the influence of the hydrodynamic contribution to the total peak dispersion, the peak variances corresponding to the Taylor dispersion, the injection plug, and the axial diffusion were calculated. This work demonstrates that peak dispersion in a capillary partially coated by the inlet end is different from that obtained when the coating is performed by the outlet end. Experimentally, the combination of a partially coated capillary with a large volume sample stacking preconcentration step can be used for injecting up to 95% of the capillary volume. This approach leads to a preconcentration factor of 60 compared with CZE with classical injection.