Thyroid-specific transcription factors TTF-1 and Pax-8 play a decisive role in the determination and maintenance of cellular phenotype activating thyroglobulin (Tg), thyroperoxidase (TPO), thyrotropin receptor (TSH-R) and the sodium/iodide symporter (NIS) gene transcription. In the present work, we have studied the expression of TTF-1 and Pax-8 and their target genes in samples derived from thyroid neoplasms of follicular origin, as well as in medullary carcinoma (MTC), obtained from surgery or from fine needle aspiration (FNA) biopsies. The results show that TTF-1 and Pax-8 are expressed in well differentiated adenomas and that their expression decreases in less differentiated papillary and follicular carcinomas and is lost in undifferentiated anaplastic carcinomas. Parallel levels of Tg, TPO and TSH-R expression were found in the same neoplasm samples. Interestingly TSH-R and TTF-1 gene expression was found in MTC samples. Furthermore, the expression of the thyroid-specific genes and their transcription factors is lost in thyroid cells derived from follicular, papillary and anaplastic human carcinomas. In these cells, Tg, TPO and TSH-R promoter activities were absent. Cotransfection with expression vectors for TTF-1 and Pax-8 resulted in the stimulation of transcription to a different extent for each promoter. These results may be clinically relevant for the evaluation and prognosis of thyroid cancer since the loss of specific markers correlates with the degree of tumor differentiation.