Ammonium transport is mediated by membrane proteins of the ubiquitous Amt/Rh family. Despite the availability of different X-ray structures that provide many insights on the ammonium permeation process, the molecular details of its mechanism remain controversial. The X-ray structures have revealed that the pore of the Amt and Rh proteins is characterized by a hydrophobic portion about 12A long in which electronic density was observed in crystallographic study of AmtB from Escherichia coli. This electronic density was initially only observed when crystals were grown in presence of ammonium salt and was thus attributed to ammonia (NH(3)) molecules, and lead the authors to suggest that the conduction mechanism in the Amt/Rh proteins involves the single-file diffusion of NH(3) molecules. However, other X-ray crystallography results and molecular mechanics simulations suggest that the pore of AmtB could also be filled with water molecules. The possible presence of water molecules in the pore lumen calls for a reassessment of the growing consensus that Amt/Rh proteins work as plain NH(3) channels. Indeed, functional experiments on plant ammonium transporters and rhesus proteins suggest a variety of permeation mechanisms including the passive diffusion of NH(3), the antiport of NH(4)(+)/H(+), the transport of NH(4)(+), or the cotransport of NH(3)/H(+). We discuss these mechanisms in light of some recent functional and simulation studies on the AmtB transporter and illustrate how they can be reconciled with the available high resolution X-ray data.