We have isolated and characterized the cDNA for eZNF, a zinc finger gene expressed in human inner ear, from a kinetically enriched human inner ear cDNA library. The sequence of full length cDNA was determined and its expression pattern characterized. A high degree of homology is shared between eZNF and rat transcription factor Kid-1. It belongs to the C2H2 class of zinc finger genes, contains a Kruppel-associated box (KRAB) domain near the N-terminus, and has consensus sites for phosphorylation. The gene is expressed in kidney and inner ear structures of mouse and human as determined by Northern blot analysis. In situ hybridization was used to demonstrate specific expression of the mouse eZNF homologue in epithelial layers of the saccule, semicircular canals, and the cochlea of newborn mice. The genomic clone corresponding to the cDNA was isolated and used for fluorescence in situ hybridization to localize it to human chromosome 5qter. The identification of genes expressed in human inner ear by representational difference analysis, their chromosomal location, and expression pattern of their homologues in developing mouse inner ear comprise a strategy that can potentially identify genes important in hearing and deafness.