The human gene encoding the thyroid transcription factor 2 (TTF-2) was cloned and mapped to human chromosome 9q22. Three polymorphisms were identified in the gene by SSCP and direct sequencing: two consist of a third base substitution in the triplet encoding Leu129 and Ser273, and the third is an alanine stretch that varies from 12 to 17 residues. TTF-2 plays a critical role during thyroid morphogenesis in mice, and in man the TITF2 gene is associated with congenital hypothyroidism and cleft palate with thyroid dysgenesis. The polymorphisms identified in this study can be used as markers to study the role of the TITF2 gene in other cases of thyroid dysgenesis, especially in familial cases.