Nuclear pore complexes (NPCs) are the rate-limiting barriers for the exchange of macromolecules (e.g. transcription factors or mRNA) between the nuclear and cytosolic compartments. NPC conformation determines movement of cargo in either direction and thus controls gene expression. ATP and calcium are known to induce an NPC shape change (increase in height and decrease in diameter) indicating pore contraction. Here we report a CO2-induced shape change which is different to the ATP/calcium response. Experiments were performed on the isolated nuclear envelope of Xenopus laevis oocytes. The nuclear envelope was spread on glass and the native cytoplasmic surface was imaged with atomic force microscopy (AFM). The preparation was scanned in a water-saturated 100% O2 atmosphere at room temperature. Exposure to 5% CO2 (95%O2) led over a time course of minutes to a dramatic NPC shape change (decrease in height and decrease in diameter) indicating pore closure. NPCs turned flat and central channel openings virtually disappeared. The CO2 response was only slowly reversible. We conclude that NPCs apparently collapse in response to CO2, a structural change that could lead to the functional isolation of the cell nucleus.