In order to investigate the effect of NaCl stress on Na+ and K+ distribution and compartmentation in salt tolerant (IR651) and sensitive(IR29) rice genotypes, a factorial experiment based on completely randomized design (CRD) with four replications was conducted in Agricultural Biotechnology Institute of Iran (ABRII) during 2006. Seeds of rice genotypes were grown in Yushida nutrient solution and treated with 0 and 100 mM NaCl, after full expansion of sixth leaves. Leaves were scored basipetally and samples were collected from root, leafsheath and leaves No. 3, 4, 5 and 6 at 0, 72, 120, 240 and 384 h after starting treatments. In addition, some attributes including, RWC, water and osmotic potentials, osmotic adjustment, total soluble sugars, Ca2+, Cl¯, and Mg2+ concentrations were measured only in leaf 6 until development of injury in this leaf (240 h after starting treatments). Results showed that salt stress declined dry weight (DW) of IR29 more than IR651 and had no significant effect on DW of older leaves while reduced DW of leaf 6 and root in both cultivars. Salt tolerant cultivar was able to compartmentize Na+ in lower leaves. Concentration of K+ reduced by salt stress in leafsheaths and roots, and had no changes in leaf 6 of both genotypes. However, osmotic adjustment was more in tolerant genotype (0.2 MPa) compare to sensitive genotype (0.03 MPa). Salinity stress increased the amount of Cl¯ and total soluble sugars, while reduced Ca2+ and Mg2+ concentrations in leaves of both genotypes. Our findings show that the IR651 has the ability to control Na+ transport to upper parts of plant, and compartmentize the Na+ in older leaves; hence it was able to reduce damage to younger leaves. This helps plant for up-regulation of other salinity tolerance mechanisms. Therefore, it is possible to use these attributes for selection of tolerant lines in rice breeding programs.