The hydrodynamics of flow through two-dimensional parallel-plate microchannels with periodic hydrophobic strips under finite Reynolds numbers is studied using dissipative particle dynamics simulations. The hydrophobic and hydrophilic regions are modeled using partial-slip and no-slip boundary conditions, respectively. We first consider channels with symmetric hydrophobic strips on both walls. It was observed that the volume flow rate through the channel is nonlinearly dependent on the area fraction of the hydrophobic strips. Next, we study flow in an antisymmetric channel in which the hydrophobic strips on the two channel walls are staggered with an axial offset. We observe that, in contrast to the symmetric channels, the presence of antisymmetric strips cause a finite velocity component towards the center of the channel. This cross-stream velocity field may potentially prove useful for separating second-phase particles or enhancing mixing in such microchannels. © 2015, Springer-Verlag Berlin Heidelberg.