Apoptosis is a physiological form of programmed cell death and crucial for normal development, tissue homeostasis, and the elimination of damaged cells. Cells committed to apoptosis strategically degrade following sequential breakdown of vital cellular organelles including the nuclear envelope (NE). The latter forms a selective transport barrier between the cytosol and the nucleus. The selectivity of this barrier, referred to as nuclear barrier, is provided by nuclear pore complexes (NPCs), large protein assemblies, which regularly perforate the NE serving as gatekeepers. The selectivity of the NPC for macromolecular transport is in turn established by unstructured 'fiber-like' proteins which allow only the transport of macromolecules that can dissolve therein. During apoptosis the barrier function of the NE is partially abolished. It is assumed that this nuclear barrier leakiness is necessary to deliver large apoptosis promoting factors into the nucleus and yet the factors causing the leakiness remain to be identified. We set out to determine these factors and addressed the question as to how they cause nuclear barrier leakiness. For this purpose, we established an in vitro assay in which apoptosis is triggered in a cytosolic extract of Xenopus laevis oocytes. Incubation of isolated oocyte nuclei in this extract rendered the NE permeable to a large macromolecule, 70 kDa FITC dextran, generally excluded from the NPC. Testing several caspase inhibitors with this assay, it turned out that both caspases 3 and 9 are required for the increase in passive NE permeability. In addition, on introduction of importin b 45-462, which plugs the NPC channel, the caspases 3,9-induced increase of NE permeability is significantly reduced. Moreover, by means of the nano-imaging and mechanical approach atomic force microscopy no ruptures in the NE structures were observed and it was thus assumed that indeed structural alterations in the NPC central channel but not ruptures in the NE are the cause for nuclear barrier leakiness. Utilising a long, sharp, high aspect ratio AFM tip, well narrower than the NPC channel, it was possible to sense the interior of the NPC channel. Indeed, it turned out that proteins have been partly removed from the NPC channel and concomitant changes in NPC structural and mechanical properties were observed. We conclude that the essential nuclear barrier leakiness during apoptosis is caused by caspases 3 and 9 and presume that they trigger the leakiness by proteolysis activity in the NPC channel which leads to a collapse of the fiber-like proteins therein.