The effect of axial flow variation on the hydrodynamic (Taylor-Aris) dispersion in a patterned microchannel consisting of periodic pillars and gaps is characterized for limiting Cassie-Baxter and Wenzel state configurations. The entry effects of flow for subsequent gaps and pillars are crucial as the flow tends towards plug flow over the gaps due to free slip at the air-liquid interface for the Cassie state or increased cross section for the Wenzel state and fully-developed parabolic flow over the pillars. The study includes analyzing the solute concentration distribution as a function of Peclet number based on the gap length, using CFD simulation and quantifying the dispersion based on Aris method of moments. For the Cassie State, simulations predict a narrower solute concentration distribution compared to flow in smooth channels. Detailed analysis reveal varied dispersion characteristics with Peclet number: similar dispersion with a time lag for low Peclet numbers and a reduced dispersion for high Peclet Number due to enhanced effect of slip. For the Wenzel state, a considerable loss of solute occurs due to the presence of dead zones within the gaps resulting in a significant increase in dispersion. The changed dispersion characteristics may have profound implications in microfluidic applications involving mixing and separation e.g., in liquid chromatography. (C) 2015 Elsevier Ltd. All rights reserved.