Recent advances in human molecular genetics have identified mutations in the TWIST, FGFR-1, FGFR-2 and FGFR-3 genes to be important causes of craniosynostosis. Despite this, however, mutations cannot be identified in the majority of patients. This study reports the first comprehensive screen of mutations in TWIST, FGFR-1, FGFR-2 and FGFR-3 genes in a cohort of patients with craniosynostosis. This has led to the identification of Saethre-Chotzen syndrome to be a new microdeletion disorder and reports the first example of a gene-environment interaction leading to craniosynostosis. In addition, investigation of the expression patterns of the Fgfr and Twist genes in the normal developing mouse coronal suture has identified the TWIST protein to be important in cranial suture initiation and biogenesis. These findings have significant clinical implications and will form the basis of future attempts to develop novel therapies aimed at inhibiting cranial suture fusion.