Several monogenic disorders result in craniosynostosis, the premature fusion of skull sutures in the neonate, causing craniofacial malformation and, occasionally, neurological compromise. These malformations were initially classified on a clinical basis, but several recent reports have clarified the underlying mutations in many of these syndromes, allowing the complexity of the relationship between mutation and resultant phenotype to be viewed more clearly. This article summarizes the current situation regarding syndromic craniosynostosis, highlights the complementarity of clinical, cytogenetic and molecular approaches that have contributed to the improved understanding of the genetic basis of craniosynostosis, and considers the new challenges that have emerged.