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In the present study, performances of parallel-flow, counter-flow, and cross-flow double layer microchannel heat sinks have been analyzed under non-uniform heating conditions.The heat sinks were evaluated numerically using conjugate heat transfer analysis by solving three-dimensional Navier-Stokes and energy equations.Water with variable themophysical properties was used as coolant.All the heat sinks consist of two layers of microchannels with 20 channels in each layer.Two layouts of non-uniform heating condition were selected, single hotspot at the center and five hotspots distributed all over the heat sink A background heat flux of 100 W/cm2 and hotspot heat flux of 500 W/cm2 were selected as heating conditions.For the single hotspot at the center, a parallel-flow design showed the lowest temperature at the hotspot whereas for the multiple hotspot condition, a cross-flow design showed better temperature uniformity at all the hotspots.