Two cochleas with permanent, noise-induced threshold shifts of 40 to 60 dB (as measured by responses of single, auditory-nerve fibers) were analyzed in detail, first at the light-microscopic level, and subsequently with transmission electron microscopy of serial sections. The light-microscopic analysis showed that there was little hair cell loss, but widespread damage to the stereocilia, especially those on the inner hair cells and first-row outer hair cells. Transmission electron microscopy revealed no pathology in any cells or organelles in the organ of Corti except for the stereocilia and their rootlets. Stereocilia tufts on first-row OHCs and IHCs were badly damaged; those on second- and third-row OHCs appeared ultrastructurally normal. Within the IHC tuft, the damage to the tall, outer row of stereocilia was often selective: the shorter rows could remain ultrastructurally normal even when the tall row was completely missing. The data suggested that most of the structures which appear normal in a careful light-microscopic analysis are also normal at the ultrastructural level. This strengthens earlier suggestions that the correlations between light-microscopic stereocilia changes and alterations in single-unit physiology are causal in nature. The most common stereocilia pathologies were fracture, attenuation or complete loss of the stereociliary rootlets, especially in the region of the cuticular plate near the endolymphatic surface of the cell. The degree and extent of these changes were well correlated with the degree and extent of stereocilia disarray. Abnormalities of the actin-filament matrix within the stereocilia were extremely rare in unfused stereocilia, however, they were common when the stereocilia were part of a fusion bundle. Fusion of stereocilia was always associated with ectopic supracuticular cytoplasm. Based on the ultrastructural observations, different sequences of structural changes preceding the generation of disarray, loss or fusion of stereocilia are suggested.