Retinal stem cells (RSCs) exist as rare pigmented ciliary epithelial cells in adult mammalian eyes. We hypothesized that RSCs are at the top of the retinal cell lineage. Thus, genes expressed early in embryonic development to establish the retinal field in forebrain neuroectoderm may play important roles in RSCs. Pax6, a paired domain and homeodomain-containing transcription factor, is one of the earliest genes expressed in the eye field and is considered a master control gene for retinal and eye development. Here, we demonstrate that Pax6 is enriched in RSCs. Inactivation of Pax6 in vivo results in loss of competent RSCs as assayed by the failure to form clonal RSC spheres from the optic vesicles of conventional Pax6 knockout embryos and from the ciliary epithelial cells of adult Pax6 conditional knockout mice. In vitro clonal inactivation of Pax6 in adult RSCs results in a serious proliferation defect, suggesting that Pax6 is required for the proliferation and expansion of RSCs.