Loss of auditory hair cells (AHCs) is a major cause of human deafness. Considerable effort has been devoted to unraveling how these mechanotransducers of sound are specified, with a view to correcting hearing loss by gene or stem cell therapies. Recent work on signaling cascades, particularly lateral inhibition and planar cell polarity, has begun to tie together some of the known pathways. Mutations in mice and humans that cause hearing and/or balance disorders are also shedding light on how AHCs are specified and, maintained and handle ion flux. Studies on some of these genes are beginning to provide insights into the more complex genetics of later onset forms of hearing loss. Progress has also been made in solving some long-term goals of auditory biology. Cadherin23 has been identified as a component of AHC stereocilia tip links, and progress has been made towards identifying the elusive AHC mechanoreceptor channel. Preliminary steps have also been taken towards inner-ear gene therapy, and in the engineering of embryonic stem cells for eventual cell therapies. Mammals cannot regenerate AHCs, but birds and other lower vertebrates can. Genomic tools have now been brought to bear on this problem with the aim of deciphering the molecular basis of this regenerative capability. The combination of new genomic tools and the many mouse and chicken embryological and genetic resources should increasingly provide new insights into how AHCs are programed and maintained.