Msx1 plays a key role in early dental and cranio-facial patterning. A systematic screening of Msx1 transcripts during late postnatal stages of development evidenced not only sense mRNA but also antisense mRNA in the skeleton. Natural antisenses are able to bind their corresponding sense RNAs and block protein expression. Specific reverse-transcription polymerase chain reaction (RT-PCR) Northern-blotting using riboprobes and primer extension analysis allowed to identify and sequence a mouse 2184-base Msx1 antisense transcript. The transcription start site was located in a region including a consensus TATA box. In situ hybridization evidenced an increase in antisense mRNA expression during dental and bone cell differentiation in prenatal (Theiler stages E15.5-18.5) and newborn mice. This upregulation was related to Msx1 protein downregulation in cells expressing Msx1 sense mRNA. In vitro, transient Msx1 sense and antisense mRNA overexpression was performed in MO6-G3 cells, which pertain to the odontoblast lineage (polarization and dentin sialoprotein and phosphoprotein synthesis). The balance between antisense and sense Msx1 mRNAs appeared to control Msx1 protein levels. These data suggest that a bidirectional transcription of Msx1 homeogene may control Msx1 protein levels, and therefore may be critical in cell communication and differentiation during dental and cranio-facial development and mineralization.