Jose M. De las Heras, Celia Garcia-Cortes, David Foronda, Jose Carlos Pastor-Pareja, L. S. Shashidhara, and Ernesto Sanchez-Herrero Although the specific form of an organ is frequently important for its function, the mechanisms underlying organ shape are largely unknown. In Drosophila , the wings and halteres, homologous appendages of the second and third thoracic segments, respectively, bear different forms: wings are flat, whereas halteres are globular, and yet both characteristic shapes are essential for a normal flight. The Hox gene Ultrabithorax ( Ubx ) governs the difference between wing and haltere development, but how Ubx function in the appendages prevents or allows flat or globular shapes is unknown. Here, we show that Ubx downregulates Matrix metalloproteinase 1 ( Mmp1 ) expression in the haltere pouch at early pupal stage, which in turn prevents the rapid clearance of Collagen IV compared with the wing disc. This difference is instrumental in determining cell shape changes, expansion of the disc and apposition of dorsal and ventral layers, all of these phenotypic traits being characteristic of wing pouch development. Our results suggest that Ubx regulates organ shape by controlling Mmp1 expression, and the extent and timing of extracellular matrix degradation.