Nitrate compartmentalization in intracellular organelles has been long recognized as critical for plant physiology but the molecular identity of the proteins involved remained unclear for a long time. In Arabidopsis thaliana, AtClC-a has been recently shown to be a NO(3)(-)/H(+) antiporter critical for nitrate transport into the vacuoles. AtClC-a is a member of the CLC protein family, whose animal and bacterial members, comprising both channels and H(+)-coupled antiporters, have been previously implicated exclusively in Cl(-) transport. Despite the different NO(3)(-) over Cl(-) selectivity of AtClC-a compared to the other CLC antiporters, it has similar transport properties. Other CLC homologues have been cloned in Arabidopsis, tobacco, rice and soybean.