Hox genes are key transcription factors for the establishment of the rostro-caudal axis in Bilaterian development. Over the course of evolution, they acquired several new functions within vertebrate- and mammalian-specific structures. Among these, Hox genes seem to be required for the correct development and function of embryonic and adult mammary glands. Members of the Hox9 paralogy group are indeed expressed in the developing mammary mesenchyme and the loss of function of Hoxd9 in lactating females caused 50% lethality of the offspring by milk starvation due to hypoplasia of the mammary glands (Chen and Capecchi, 1999). In this study, we characterized the transcription profiles of embryonic mammary glands to globally describe their Hoxome. Interestingly, Hoxd9 is the only Hoxd gene significantly expressed in the mammary bud. We identified a 20kb large region located approximately 300kb downstream the HoxD cluster and containing seven evolutionary conserved sequences. This DNA segment is essential to drive expression of Hoxd9 in the mammary bud.