Progress in the structure determination of AQPs has led to a deep understanding of water and solute permeation by these small integral membrane proteins. The atomic structures now available have allowed the water permeation and exclusion of protons to be monitored by molecular dynamics simulations, and have provided a framework for assessing the water and solute permeation in great detail by site-directed mutations. In spite of this, further structural and molecular dynamics analyses are required to elucidate the basis for regulation as well as for gas permeation, processes that are still to be deciphered.