Oesophageal atresia and tracheo-oesophageal fistula are relatively frequently occurring foregut malformations of which the aetiology and pathogenesis are poorly understood. Recent results of molecular genetic studies, in particular the use of single and compound mutant mice, have yielded a tremendous increase in the understanding of the molecular mechanisms involved in normal and abnormal foregut morphogenesis. In the introduction of this paper, we review the very early stages of normal and abnormal embryology of the foregut derivatives and the separation of the foregut into a ventral respiratory part and a dorsal digestive part. After that, we describe the genes that have been demonstrated to play an important role in these processes.