The apoptotic removal of superfluous neurons during early brain development is strongly regulated by neuronal activity. This suggests that with emergent neuronal network activity cell death unfolds with precise temporal control but also in a region- and cell-specific manner. In order to map programmed death in the developing mouse cerebral cortex, tissue clearing, immunohistochemistry and light sheet microscopy were applied. Activated-caspase-3 (aCasp3), nuclear SYTOX as well as 5-HTT signals were then used to register the distribution of apoptotic cells across cortical regions and layers.While neocortical size steadily increased by about 7-fold from P0 to P10, the number of aCasp3-positive cells in the cortex peaked only from P4 to P7. Cumulatively, about half a million cortical neurons died until P10. At its peak, density of cell death revealed a medial-to-lateral as well as a strong dorsal-to-ventral gradient. Mapping the localization of the dying cells to functional cortical regions showed that the attenuation of apoptosis during the second postnatal week is more pronounced in granular cortical regions. In line, aCasp3-positive cell counts significantly decreased in the second postnatal week in the somatosensory cortex barrel field but not in the primary motor cortex; and this reduction was most prominent for layer 4 and layer 5 neurons.Overall, this study provides a spatiotemporal overview of cortical cell death, and potentially suggests that direct inputs to thalamorecipient cortical regions are neuroprotective at an early phase of development.