Nuclear pore complexes (NPCs) are supramolecular structures, which mediate exchange of macromolecules and inorganic ions between nucleus and cytosol. Whereas the route of macromolecules is the NPC central channel, the pathway for small ions is less clear. Here we tested the hypothesis of two separate pathways by combining structural NPC imaging with atomic force microscopy (AFM) and NPC electrical conductivity measurements. Methods: (i) Using the nuclear hourglass technique we exposed isolated Xenopus laevis oocyte nuclei to an electric field in presence of bovine serum albumine (BSA). BSA moved along this field and decorated the NPCs at the sites of the electrical current flow. Those sites were imaged afterwards by AFM. (ii) We exposed isolated nuclei to a fragment of importin b, a genetically modified nuclear import factor which irreversibly plugs the NPC central channel. In such nuclei the NPC electrical conductivity was measured and, subsequently, plugged NPCs were visualized by AFM. Results: (i) AFM imaging detected BSA molecules at the cytoplasmic NPC ring surface but not in the NPC central channel. (ii) Importin b was clearly localized in the NPC central channel while electrical NPC conductivity was not reduced. Conclusions: As indicated by the electrophoretic movement of negatively charged BSA, inorganic ions move through the NPC ring but not through the large central channel.