PAX6 function was first identified through aniridia-associated null mutations. Since then, this transcription factor, with a paired domain and a homeodomain, has become a paradigm, illustrating functional conservation in developmental pathways. The Small eye mouse and Drosophila eyeless have served as major model systems in defining the multistage roles for Pax6 in eye and olfactory system development throughout evolution. The overt phenotypic consequences of heterozygous human and mouse Pax6 mutations were initially confined to the eye, with some interesting genotype-phenotype correlations being noted. Recently, structural and functional abnormalities in the olfactory system have been identified. Alterations in brain structure have also been documented, in line with the wider forebrain and cerebellar expression of Pax6. The broad PAX6 expression pattern is controlled by a number of long-range control elements, and is reflected in the severe homozygote phenotype. Upstream regulators and a multitude of downstream targets of PAX6 have been identified, and its varied tissue-specific functions are emerging.