In this review we focus on studies using atomic force microscopy (AFM) to d
escribe the function of nuclear pore complexes (NPC). After a short introdu
ction of AFM we follow the route of cargo molecules from the cytosol into t
he nucleus. AFM visualizes cargo before translocation into the nucleoplasm,
cargo docking at the cytoplasmic NPC surface, cargo passing through the NP
C and changes in NPC conformation in response to ATP, Calcium and pH. We di
scuss AFM experiments on nuclear envelopes on the basis of previous data ob
tained with more conventional techniques such as electron microscopy, confo
cal microscopy and other imaging techniques. Finally we draw attention to t
he recently developed nuclear hourglass technique that serves as a new elec
trophysiological approach to studying the structure-function relationship o
f NPC in combination with AFM at a molecular level.