Hair cells contain a single primary cilium early in development, known as the kinocilium. This cilium is usually lost in auditory hair cells but maintained in vestibular hair cells. Hair cells also possess rows of actin-based stereocilia that are responsible for responses to mechanical stimuli. The kinocilium is located adjacent to the tallest stereocilia row. In hair cells, the primary function of cilia genes is believed to be in the development of stereocilia polarity indirectly through regulation of kinocilia. Through a screen for mutations that confer resistance to aminoglycoside-induced hair cell death we have identified a number of mutations in cilia genes, showing a novel role of cilia genes in hair cells. We found that mutations in the intraflagellar transport (IFT) genes ift88, traf3ip, dync2h1 and wdr35 all lead to strong resistance to neomycin-induced hair cell death. Mutations in the transition zone genes cc2d2a, mks1, and cep290 lead to more moderate protection. These two classes of genes appear to play different roles in aminoglycoside-induced hair cell death. Mutations in IFT, but not transition zone, show a reduction of neomycin uptake into hair cells, loss of kinocilia and a reduction in control hair cell numbers. The individual IFT genes appear to differently affect hair cells as well, as mutations in ift88, traf3ip and dync2h1, but not wdr35 show a reduction in hair cell FM1-43 uptake, a process dependent upon mechanotransduction activity. This does not appear to be due to defects in stereocilia morphology. Future work will focus on delineating the mechanisms behind the diverse roles cilia genes play in hair cells.