PAX6 is the most researched of the Pax genes and appears throughout the literature as a "master control" gene for the development of eyes and other sensory organs, certain neural and epidermal tissues as well as other homologous structures, usually derived from ectodermal tissues. This transcription factor is most famous for its use in the interspecifically induced expression of ectopic eyes and is of medical importance because heterozygous mutants produce a wide spectrum of ocular defects such as Aniridia in humans.

PAX6 protein function is highly conserved across bilaterian species, for instance mouse PAX6 can trigger eye development in Drosophila melanogaster.