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It is important to properly identify aggressive tumors among differentiated thyroid cancers that are most often indolent. By comparison of a tumorigenic clone with an originally less tumorigenic papillary thyroid carcinoma (PTC) cell line, we looked for markers involved in the aggressive biology of thyroid cancer. Human PTC cell lines BHP10-3 and its tumorigenic subclone BHP10-3SCmice were compared using microarray analysis. Upregulated genes in the tumorigenic clone were selected for RT-PCR, immunoblot analysis and immunohistochemistry in human tissue. Hypoxia-inducible factor (HIF)-1α and its chaperone protein heat shock protein (HSP)90 showed significantly increased expression in BHP10-3SCmice and human PTC tissue. These two genes, HIF-1α and HSP90, were further validated using siRNA gene knockdown, pharmacological inhibition using 17-N-allylamino-17-demethoxygeldanamycin (17-AAG), an inhibitor of both HSP90 and HIF-1α and in vivo orthotopic animal model. Invasiveness of BHP10-3SCmice was abrogated by blockade of HIF-1αin vitro by both siRNA and 17-AAG. The same finding was demonstrated in the orthotopic animal model. These findings support that HIF-1α is important in tumorigenesis of PTC and that it may serve to be an important target for identification and treatment of aggressive tumors. (Cancer Sci 2012; 103: 464–471)