The core problem in craniofacial development is regional specification of cell-specific gene expression. Regional specification is also referred to as pattern formation or spatial organization. During early embryogenesis, regional specification is possibly operant following blastula, and is apparent during gastrulation and thereafter during embryonic and fetal stages of development. Current interdisciplinary approaches toward understanding embryonic development incorporate a number of scientific approaches including those of recombinant DNA technology. Three major advances have significantly enhanced the utility of so-called "genetic engineering," including the discovery of restriction nuclease enzymes that cleave DNA sequences at specific sites; the discovery of DNA ligase enzymes that facilitate ligation and annealing of DNA sequences to one another, so as to facilitate the joining of foreign DNA sequences with host DNA; and the discovery of effective techniques for the introduction of foreign DNA sequences into previously refractory organisms. The present discussion analyzes the problem of regional specification of ameloblast-specific gene expression as a paradigm for utilizing recombinant DNA technology in studies of normal and abnormal craniofacial development.