To identify changes in gene expression associated with tumor progression and metastasis in vivo, we investigated differential gene expression in a metastatic squamous carcinoma model established in syngeneic mice, including a tumorigenic line PAM 212, and metastatic sublines derived from PAM 212 tumors, using mRNA differential display (DD) and cDNA microarrays. Using DD, seventy-two candidate cDNAs were detected, and thirty-four cDNAs were confirmed to be differentially expressed by northern blotting analysis. Global mRNA expression profiles were generated using an NCI mouse Oncochip composed of four thousand elements representing known genes and ESTs, plus 57 of the candidate cDNAs detected by DD to facilitate data validation. Clustering analysis of array results from metastatic cell lines and tumors identified a subset of genes that exhibited increased expression in the metastases, revealed that 22 unique clones are highly homologous to previously identified genes, and nine novel cDNAs. Strikingly, 10/22 of the genes identified have been associated with activation of the Nuclear Factor-kB signal transduction pathway. One of the genes identified, Gro-1, was recently confirmed to promote tumor growth, metastasis and angiogenesis of SCC in vivo in a separate report. These results demonstrate that early response pathway components and down stream genes related to NF-κB are expressed with metastatic tumor progression. Functional genomic approaches may promote a better understanding of the repertoire of related genes and molecular pathways involved in tumor progression and metastasis.