The cooling of three-dimensional electronic chip assemblies (stacks) is one of the most serious challenges facing the electronics industry as it moves toward fabrication approaches combining speed with energy efficiency. Here we show that by generating vortical microscale flows taking advantage of the inherent presence of Through Silicon Vias (TSV) in 3D integrated liquid (water) cooling of chip stacks, both large heat transfer enhancement as well as significantly better temperature uniformity can be accomplished. The approach is demonstrated experimentally in heat sinks consisting of a microcavity confining micropin fin arrays, mimicking TSV. Flow fluctuations and vortex shedding were triggered at specific Reynolds numbers, which are functions of the pin geometries and level of confinement. The resulting heat transfer enhancement due to the vortex-induced fluctuations and mixing, yields local Nusselt number increases up to 230% thereby reducing the chip temperature non-uniformity almost by a factor of three. The vortex shedding also induces a pressure drop increase. Remarkably, the effective improvement in the thermal performance due to vortex shedding, even after factoring in the rise in pumping power, reaches a peak value of 190%. Analysis of instantaneous liquid temperature signatures of shed microvortices using micron-resolution laser-induced fluorescence (μLIF), proved them to be the reason for both the elimination of liquid hotspots and the exceptional augmentation in heat transfer. These findings have important implications in the design of the new generation of integrated, out of plane electronics cooling with liquids. © 2013 Elsevier Ltd. All rights reserved.