A three-dimensional computational model was developed to investigate the effect of synthetic jet interaction with cross flow in micro-channel on the cooling of microchip. A range of parametric studies by varying heat fluxes at the surface of the top of the silicon wafer and membrane oscillating amplitudes was conducted. The resulting complex, conjugate heat transfer through the silicon substrate was analysed. When the actuator was switched on, noticeable temperature drop was observed at all points in the substrate. Quasi steady states have been reached for the presented results which indicated the available cooling potential of single synthetic jet actuator. (C) 2011 Elsevier Ltd. All rights reserved.