Significant advances in the study of the human face have revealed the genetic and gene-environment bases of numerous common and rare craniofacial disorders. Classification of craniofacial malformations based on clinical phenotypes is sometimes quite different from the genetic findings of patients. Different mutations in a single gene can cause distinct syndromes, and mutations in different genes can cause the same syndrome. The extracellular signaling molecule SHH, fibroblast growth factor receptors, and transcription factors GLI3, MSX2, and TWIST are discussed as examples of molecules involved in interrelated signal transduction networks regulating craniofacial development. Progress in the understanding of normal and abnormal craniofacial development, through the study of morphoregulatory signaling pathways, has benefited from multifactorial approaches recommended 40 years ago at the National Institute of Dental Research-sponsored landmark Gatlinburg Conference. The utilization of biochemistry, protein structure analyses, tissue culture, and animal model systems for developmental genetics has resulted in remarkable scientific advances. The evolutionary conservation of morphoregulatory pathways has revealed the homology of genes associated with human craniofacial malformations and their counterparts that regulate the morphogenesis of fruit flies. The continued investments in basic, translational, and patient-oriented research regarding normal and abnormal craniofacial development will translate into substantial improvements in the prevention, diagnosis, and treatment of craniofacial diseases and disorders.