The SLC24 gene family encodes K(+)-dependent Na(+)-Ca(2+) exchangers or NCKX proteins. The NCKX4 and NCKX5 isoforms have been shown to be important for pigmentation, and single nucleotide polymorphism (SNP) in both alleles of the SLC24a5 gene is the major genetic determinant for light skin in Caucasians. NCKX4 is thought to operate in the surface membrane of cells, whereas NCKX5 is thought to be located in intracellular membranes. However, no functional data have yet been reported to describe either NCKX4 or NCKX5 activity in pigmented cells. In this study, we used the B16 and MEB4 mouse pigmented cell lines to investigate NCKX-mediated Ca(2+) fluxes using (45)Ca uptake experiments and measurements of changes in intracellular free Ca(2+) with the fluorescent Ca(2+)-indicating dye Fluo-4. We used siRNA-mediated knockdown to selectively reduce either NCKX4 or NCKX5 expression. The results show that both B16 and MEB4 cells contain roughly equal amounts of NCKX4 and NCKX5 transcript, but surface membrane NCKX activity is restricted to NCKX4. Intracellular NCKX4 activity was also observed, but we could not unambiguously detect any NCKX5 activity. We were able to demonstrate that NCKX5 is a functional K(+)-dependent Na(+)-Ca(2+) exchanger located in internal membranes after transfection of NCKX5 cDNA in HEK293 cells. We conclude that pigment cells express robust, functional NCKX4 activity, but that the role of NCKX5 remains enigmatic ten years after the discovery of its link to pigmentation.