The molecular biology of the homeobox genes MSX1 and MSX2 is reviewed. In a selective type of tooth agenesis, an MSX1 G --> C transversion results in a missense mutation Arg31Pro. The phenotype is due to haploinsufficiency. Boston-type craniosynostosis involves an MSX2 C --> A transversion, resulting in a missense mutation Pro7His. Three different mutations on MSX2 cause parietal foramina by haploinsufficiency. These mutations, which result in decreased parietal ossification, are in marked contrast to the gain-of-function mutation for Boston-type craniosynostosis, which results in increased sutural ossification.