Cadherins are components of adherens junctions and play critical roles during embryogenesis and organogenesis. They interact through the formation of anti-parallel dimers to mediate cell adhesion, migration and compaction. We recently showed that cadherins also play important roles in the inner ear; mutations in cadherin 23 (Cdh23) disrupt stereocilia organization on hair cells leading to deafness and vestibular dysfunction in waltzer mice. Here we extend our initial study on the structure and function of Cdh23. The mouse Cdh23 locus is comprised of two 5'-untranslated exons and 69 coding exons; together they cover a genomic distance of at least 350 kb. Amino acid sequence alignments and secondary structure prediction suggest that Cdh23 ectodomains adopt a conformation similar to the classic cadherins. Nucleotide sequence analysis of six alleles of waltzer reveals a strong correlation between loss of function mutations and the deafness/waltzing phenotype. A Cdh23 transcript with a spliced exon 68 is the predominantly expressed isoform in the organ of Corti. Age-related hearing loss (Ahl) is a non-syndromic trait in common inbred strains of mice associated with the Ahl locus on chromosome 10. Sequence comparison of Cdh23 between C57BL/6J and CAST/Ei identified ten amino acid polymorphisms. In the 5'- and 3'-untranslated regions we detected 11 single nucleotide polymorphisms. None of these sequence changes correlate with the Ahl phenotype. Our results provide the necessary framework for further characterization of Cdh23-related hearing loss in mice.