The elucidation of the molecular mechanisms underlying the very early steps of thyroid organogenesis and the etiology of most cases of thyroid dysgenesis are poorly understood. Many genes have been identified as important contributors to survival, proliferation and migration of thyroid cells precursors, acting as an integrated and complex regulatory network. Moreover, by generation of mouse mutants, the studies have provided better knowledge of the role of these genes in the thyroid morphogenesis. In addition, it is likely that a subset of patients has thyroid dysgenesis as a result of mutations in regulatory genes expressed during embryogenesis. This review summarizes molecular aspects of thyroid development, describes the animal models and phenotypes known to date and provides information about novel insights into the ontogeny and pathogenesis of human thyroid dysgenesis.