Synchondrosis is defined as the development of a union between two bones by the formation of either hyaline cartilage or fibro-cartilage. This paper reviews the relationship between cranial base synchondroses and craniofacial development. The cranial base synchondroses are important growth centers of the craniofacial skeleton. Their abnormalities lead to numerous growth and developmental conditions in the craniofacial region. In dentofacial orthopedics, mechanical forces are commonly applied to cranial bones for growth modification to treat such conditions. Molecular biology and genetics provide tools to investigate the molecular mechanisms, genes and transcription factors responsible for synchondrosis and craniofacial development.