The dramatic opportunities presented by comprehensive gene profiling technologies are curbed by the problem of segregating these large amounts of gene expression data into meaningful categories for study. This is particularly evident in infiltrating carcinomas of the pancreas, in which global gene expression data primarily mirrors the prominent desmoplastic response to the infiltrating neoplasm. In an effort to better characterize the gene expression of invasive pancreatic cancers and their associated desmoplastic response, we performed in situ hybridization on pancreatic cancer tissues to characterize the expression of 12 genes identified by serial analysis of gene expression as highly expressed in invasive pancreatic cancer tissues but not in pancreatic cancer cell lines. In situ hybridization demonstrated that eight genes were expressed within the stromal and/or angioendothelial cells of the desmoplastic response to the invasive tumor, and four of these genes were specifically expressed by the stromal cells immediately adjacent to the invasive neoplastic epithelium, suggesting regional differences in gene expression within the host desmoplastic response. In contrast, four genes were specifically expressed by the invasive neoplastic epithelium, indicating important differences between in vivo and in vitro gene expression of human epithelial neoplasms. We have identified a highly organized structure of gene expression within the host stromal response to invasive pancreatic cancer that may reflect tumor-host communication and serve as a target for therapeutic intervention.