In this paper, the effect of slip length on entropy generation of fluid flow in a microchannel is analyzed. The flow between the parallel plates is considered fully developed both hydrodynamically and thermally. Uniform heat flux boundary condition is assumed. The fluid is supposed to be non Newtonian, following a power law model. To model the slip, Navier's linear slip law has been used. The spatial distribution of fluid velocity, non dimensional temperature, non dimensional entropy generation and Bejan number has been investigated for different slip length ratios. For dilatants fluids, it is found that that the effect of slip length is significant and cannot be neglected.