Previously, we reported that renal active calcium-transporting genes are highly expressed in female mice and suggested that renal calcium-processing genes play a critical role in normal calcium reabsorption in females (Lee GS, Lee KY, Choi KC, Ryu YH, Paik SG, Oh GT, Jeung EB. J Bone Miner Res 22: 1968-1978, 2007). In the current study, we evaluated the differential expression of renal calcium-processing genes in male and female mice. Using microarray analysis, we identified K(+)-dependent Na(+)/Ca(2+) exchanger 3 (NCKX3) as a gene that was differentially expressed in the kidneys of female and male mice. The expression levels of renal NCKX3 mRNA and protein were higher in female than in male mice, whereas there was no difference between the genders in the levels of NCKX3 expression in the brain. Renal NCKX3 localized to the basolateral layer of distal convoluted tubules, indicating that this protein participates in renal calcium reabsorption. To identify putative regulators in the gender-specific expression of NCKX3, several hormones were injected into mature female and male mice. Although any hormones did not alter NCKX3 expression, adrenal gland-secreted hormones aldosterone and hydrocortisone did downregulate renal NCKX3 mRNA expression in female mice, but they did not change its protein levels. Taken together, the results in this study suggest that a high level of renal NCKX3 expression maintain in distal convoluted tubules may play a role in active calcium transport in the kidneys of female mice.