ABSTRACT: CCD, which is characterized by hypoplastic clavicles, open fontanelles, supernumerary teeth, and short stature, are caused by heterozygous mutation of RUNX2. However, the reason why the suture closure is severely impaired in CCD patients remains to be clarified. The closure of posterior frontal (PF) and sagittal sutures was completely interrupted in Runx2+/– mice, and the proliferation of the suture mesenchymal cells was reduced compared with that in wild-type mice. To reveal the molecular mechanism, the differentially expressed genes between wild-type and Runx2+/– PF sutures were identified by microarray and real-time RT-PCR analyses. The expression of hedgehog, Fgf, Wnt, Pthlh signaling pathway genes, including Gli1, Ptch1, Ihh, Fgfr1-3, Tcf7, Wnt10b, Wnt1, and Pth1r, was reduced in PF sutures of Runx2+/– mice. These findings indicated that more than half dosage of Runx2 is required for the proliferation of suture mesenchymal cells, their commitment into osteoblast-lineage cells, and the induction of the hedgehog, Fgf, Wnt, and Pthlh signaling pathway gene expression in the sutures.