Information on gene alterations associated to poorly differentiated (PDTC) and anaplastic thyroid carcinomas (ATC) is scarce. Using human cancer cell lines as a tool for gene discovery, we performed a cytogenetic and oligo-array analysis in five new cell lines derived from two PDTC and three ATC. In PDTC we evidenced, as important, the involvement of the MAPK/ERK kinase pathway, and downregulation of a group of suppressor genes that include E-cadherin. In ATC, downregulation of a specific group of oncosuppressor genes was also observed. Our ATC cell lines presented chromosomal markers of gene amplification, and we were able to identify for the first time the nature of the involved amplicon target genes. We found that the main molecular differences between the two cell line types were related to signal transduction pathways, cell adhesion and motility process. TaqMan experiments performed for five amplicon target genes and for two genes, which allowed a clear distinction between ATC and PDTC: CDH13 and PLAU corroborated array results, not only in the cell lines, but also in an additional set of primary 14 PDTC and three ATC. We suggest that our findings may represent new tools for the development of more effective therapies to the hitherto untreatable ATC. Thyroid malignant neoplasms of follicular cell origin are classified into four main categories: the differentiated papillary (PTC) and follicular (FTC) carcinomas, the poorly differentiated (PDTC) and the undifferentiated or anaplastic (ATC) carcinomas. The differentiated forms are the most common. Poorly differentiated thyroid carcinomas and ATC account for only 5 -10% of the follicular malignancies; however, although rare, they represent a major challenge in oncology as they have a high morbidity and mortality rate (DeLelllis and Williams, 2004).In recent years some progress has been obtained in the identification of the genomic changes associated to the pathogenesis of DTC. In PTC, it is now clear that, in a substantially fraction of tumours, malignant transformation takes place through the constitutive activation of effectors along the MAPK/ERK kinase pathway (Mellilo et al, 2005), and in FTC, the PAX8/PPRAg fusion gene was determined to be an important event in the development of a subset of these carcinomas (Lacroix et al, 2005). At variance, the genetic information concerning PDTC and ATC is very limited. Only 27 PDTC have been evaluated by comparative genomic hybridisation (CGH) analysis, and as far as we are aware, there are no microarray studies on this entity (Wreesmann et al, 2002;Rodrigues et al, 2004). In ATC, it was demonstrated that TP53 (Wynford-Thomas, 1997) and b-catenin (Garcia-Rostan et al, 1999) mutations as well as the overexpression of OEATC1 (Mizutani et al, 2005) and AURKB (Sorrentino et al, 2005) were associated with ATC phenotype. These genes were demonstrated to be key effectors in anaplastic transformation, being responsible for evasion to apoptosis, enhanced tumour growth and replicative potential. However, although all efforts ma...