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The molecular cascades that control craniofacial development have until recently been little understood. The paucity of data that exists has in part been due to the complexity of the head, which is the most intricate regions of the body. However, the generation of mouse mutants and the identification of gene mutations that cause human craniofacial syndromes, together with classical embryological approaches in other species, have given significant insight into how the head develops. These studies have emphasized how unique the head actually is, with each individual part governed by a distinct set of signalling interactions, again demonstrating the complexity of this region of the body. This review discussed the tissue and molecular interactions that control each region of the head. The processes that control neural tube closure together with correct development of the skull, midline patterning, neural crest generation and migration, outgrowth, patterning, and differentiation of the facial primordia and the branchial arches are thus discussed. Defects in these processes result in a number of human syndromes such as exencephaly, holoprosencephaly, musculoskeletal dysplasias, first arch syndromes such as Riegers and Treacher-Collins syndrome, and neural crest dysplasias such as DiGeorge syndrome. Our current knowledge of the genes responsible for these human syndromes together with how the head develops, is rapidly advancing so that we will soon understand the complex set of molecular and tissue interactions that build a head.