With the advance of miniaturization technology, more and more electronic components are placed onto small electronic chips. This leads to the generation of high amounts of thermal energy that should be removed for the safe operation of these electronic components. Microchannel heat sinks, where electronic chips are liquid cooled instead of the conventional air cooling techniques, were proposed as a means to improve cooling rates. Later on, double layer micro channel heat sinks were suggested as an upgrade to single layer microchannel heat sinks with a better thermal performance. In the present study the effects of increasing the number of layers of the microchannel heat sink to three-layers as well as the effect of changing the flow arrangements (counter and parallel flows) within the three channel layers on the thermal performance of the heat sink were investigated. In all investigated cases the temperature distribution over the base of the microchannel heat sink system and the total pressure drop are reported. A range of mass flow rates from 1×10⁻⁴ to 5×10⁻⁴ kg/s was considered. Uniform heat flux conditions were considered during the study. COMSOL Multiphysics finite element package was employed for the numerical analysis. Results indicate significant enhancement in the uniformity of the temperature on the processor surface when multi-layer channels were employed, compared to the single-layer case. The uniformity in the temperature distribution was accompanied by reduction of pressure drop across channels for the same mass flow rate and heat flux conditions. The counter flow arrangement showed the best temperature distribution with the uniform heat flux cases.