A numerical study of 3D electrokinetic flows through micromixers was performed. The micromixers considered here consisted of heterogeneous rectangular microchannels with prescribed patterns of zeta-potential at their walls. Numerical simulation of electroosmotic flows within heterogeneous channels requires solution of the Navier-Stokes, Ernest-Plank and species concentration equations. It is known that a 3D solution of these equations is computationally very intensive. Therefore, the well-known Helmholtz-Smoluchowski model is often used in numerical simulation of electroosmotic flows. According to 2D studies on electrokinetic mixing inside heterogeneous channels, existence of vortices within the flow field always increases mixing performance. Hence, it may be expected that similar observations pertain to mixing in 3D flows as well. However, investigations on 3D micromixers identified situations in which existence of vortices had little or no significant benefit to the mixing performance. Findings of the present work indicated degree of flow asymmetry as a key parameter for the mixing performance. Since 3D flows are more capable of developing asymmetrical flow patterns, they are expected to have better mixing performance than their 2D counterparts. The results presented here for different 3D cases showed that mixing performance could be improved significantly depending on the alignment of vortex plane relative to the mixing interface of the fluids. These observations confirmed that 2D simulations of mixing could not fully explain behavior of passive micromixers.