The congenital hypothyroid (hyt/hyt) mouse has been described as having a homozygous recessive mutation of a single locus on chromosome 12 which results in significant endocrine hypofunction and retarded growth. Although a distinct correlation between inherited hypothyroidism and hearing loss in humans exists, there has been no previous evaluation of the auditory system in these mutant mice. We determined hearing thresholds by auditory-evoked brainstem response testing and noted a 40-45 dB elevation in the hyt/hyt mouse compared to littermate heterozygote (hyt/+) animals and normal progenitor controls BALB/cByJ (+/+). Conventional light microscopy was used to examine the general anatomy of the cochlea in these animals, and the surface structure of the organ of Corti was further evaluated with scanning electron microscopy. Heterozygote and normal control mice had no significant abnormalities of the cochlea, however the hyt/hyt mice displayed consistent morphologic abnormalities of the stereocilia on both inner and outer hair cell systems. The surrounding and supporting cells were identified in the cochleas of the hypothyroid mouse and control animals and showed no significant histologic abnormalities. The auditory, histologic, and ultrastructural characterization of this model provides a foundation for evaluating the effects of true inherited hypothyroidism on auditory pathway development.