Vacuolar compartmentation of Na(+) is an essential mechanism for salinity tolerance since it lowers cytosolic Na(+) levels while contributing to osmotic adjustment for cell turgor and expansion. The AtNHX1 protein of Arabidopsis thaliana substituted functionally for ScNHX1, the endosomal Na(+)/H(+) antiporter of yeast. Ion tolerance conferred by AtNHX1 and ScNHX1 correlated with ion uptake into an intracellular pool that was energetically dependent on the vacuolar (H(+))ATPase. AtNHX1 localized to vacuolar membrane fractions of yeast. Hence, both transporters share an evolutionarily conserved function in Na(+) compartmentation. AtNHX1 mRNA levels were upregulated by ABA and NaCl treatment in leaf but not in root tissue.