The plant hormone auxin plays a role in virtually every aspect of plant growth and development. Temporal and spatial distribution of auxin largely depends on the dynamic expression and subcellular localization of the PIN auxin-efflux carrier proteins. We show here that the Arabidopsis thaliana JAGGED LATERAL ORGAN (JLO) gene, a member of the LATERAL ORGAN BOUNDARY DOMAIN (LBD) gene family, is required for coordinated cell division during embryogenesis. JLO promotes expression of several PINFORMED (PIN) genes during embryonic and root development. Inducible JLO misexpression reveals that JLO activity is sufficient for rapid and high level PIN1 and PIN3 transcription. Genes of the PLETHORA (PLT) family respond to auxin and direct PIN expression, but PLT genes were severely underexpressed in jlo mutants. JLO controls embryonic patterning together with the auxin dependent MONOPTEROS/BODENLOS pathway, but is itself only mildly auxin inducible. We further show that all known auxin responses in the root require JLO activity. We thereby identify JLO as a central regulator of auxin distribution and signaling throughout plant development.