In plants the dorsoventral boundary of leaves defines an axis of symmetry through the centre of the organ separating the future top (dorsal) and bottom (ventral) tissues. Although the positioning of this boundary is critical for leaf morphogenesis, the mechanism by which it is established has not been determined. Here we show that dorsoventral boundaries in leaves derive from a boundary between Class III homeodomain-leucine zipper and KANADI expression in the shoot apical meristem, confirming that leaf founder cells are pre-patterned with respect to their dorsoventral axis. Furthermore, perturbation of this boundary not only alters leaf orientation and morphogenesis but also organ position, revealing a general role for these boundaries in plant development. Lastly, we show that auxin stabilizes boundary position at organ inception and that wounds disrupt this process. Overall our findings reveal a two-way interaction between cell type boundaries and auxin that controls fundamental aspects of plant architecture.