Pancreatic cancer is known to be an extremely lethal neoplasm, one of the reasons being that pancreatic cancer itself has an extremely high potential of invasion-metastasis. In our previous study, two pancreatic cancer cell lines with a different potential for invasion-metastasis, PC-1 with a low potential and PC-1.0 with a high potential of invasion-metastasis after intrapancreatic transplantation, were established in a Syrian golden hamster. To determine the invasion-metastasis-related factors, a cDNA microarray that represented a set of 27,000 genes was hybridized with a labeled cDNA probe and screened for molecular profiling analysis. Furthermore, Gene Ontology and Pathway differential expression of candidate genes was further validated using RT-PCR. One hundred and forty-one differentially expressed genes (>3.0-fold change) were identified in the present study, including 46 up-regulated genes (e.g., nup107, tjp-2 and MMP-13) and 95 down-regulated genes (e.g., Spc21, plau and CD44) in the PC-1.0 cells. Our present results suggest that a highly organized and structured process of tumor invasion-metastasis exists in the pancreas. Analysis of gene expression profiles by cDNA microarray provides useful information for clarifying the mechanism underlying this invasion and metastasis. Furthermore, the identification of invasion-metastasis-specific genes may allow us to develop new therapeutic and diagnostic targets for the invasion-metastasis of pancreatic cancer.