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Microchannel heat sinks are widely regarded as being amongst the most effective heat removal techniques from the space constrained electronic devices. Electronic components and chips are often subjected to spatially varying heat fluxes and hot spots in certain regions. In the present work, effects of non-uniform base heating on the performance of stacked microchannel heat sinks cooled by forced circulated water is analyzed. Finite element method is used for the analysis wherein a self developed 12 noded element is used for channel discretization. Different types of non-uniform base heating such as non-uniform heating in the ascending and descending orders with respect to the coolant flow direction in the bottom channel, upstream half heating, downstream half heating and center half heating (similar to central hotspot) are analyzed for both parallel flow and counter flow models. The results are compared with the case of uniform heating throughout the base.