Paired box protein 6 (PAX6) is a master regulator of the eye development. Over the last past two decades, our understanding of eye development, especially the molecular function of PAX6, has focused on transcriptional control of the Pax6 expression. However, other regulatory mechanisms for gene expression, including alternative splicing (AS), have been understudied in the eye development. Recent findings suggest that two PAX6 isoforms generated by AS of Pax6 pre-mRNA may play previously underappreciated role(s) during eye development, especially, the corneal development.