A key protein in the production and in the maintenance of the endocochlear potential is the Na,K-ATPase. Previously, we have shown that FXYD6 is a modulator of the Na,K-ATPase expressed in the inner ear (Delprat et al. [2007] J Biol Chem 282:7450-7456). To investigate the potential role of FXYD6 in inner ear function, we studied the developmental expression of FXYD6. Reverse transcriptase-polymerase chain reaction analysis demonstrates that FXYD6 is present as two splice variants. Both variants coimmunoprecipitate with Na,K-ATPase after expression in Xenopus oocytes. Immunohistochemistry of the cochlea (from birth to postnatal day 30) shows that FXYD6 is expressed in several epithelial cells important for endolymph homeostasis. Marked similarities were found in the developmental expression patterns of FXYD6 and Na,K-ATPase, suggesting functional cooperation between the two proteins in the generation and maintenance of the endocochlear potential and ion composition of the endolymph.