The Pax gene family encodes a group of transcription factors that have been conserved through millions of years of evolution and play roles in early development. Pax proteins have been implicated as regulators of organogenesis and as key factors in maintaining pluripotency of stem cell populations during development. Mutations of the Pax genes cause profound developmental defects in organisms as diverse as flies, mice and humans. Here, we review crucial and illustrative roles of Pax gene products in cell-fate specification and developmental biology.