Salinity is a major abiotic stress in agriculture. Here, we report that SODIUM POTASSIUM ROOT DEFECTIVE3 (NaKR3), which encodes a heavy metal-associated domain protein, is involved in salt tolerance in Arabidopsis. The results of quantitative reverse transcription-polymerase chain reaction analysis revealed that NaKR3 was induced by high salinity and osmotic stresses, but not by Cu(2+) stress. Transient expression of NaKR3-GFP in Arabidopsis protoplasts showed that the NaKR3 protein was localized in the cytosol. Transgenic Arabidopsis plants constitutively expressing NaKR3 under the control of the cauliflower mosaic virus 35S promoter exhibited increased tolerance to salt treatment. Furthermore, overexpression of NaKR3 increased the expression of SOS1 and SOS3, but decreased the accumulation of salt-induced proline. Taken together, our results indicate that NaKR3 is involved in the salt stress response in Arabidopsis.