The molecular pathology of precursor lesions leading to invasive pancreatic ductal adenocarcinomas remains relatively unknown. We have applied cDNA microarray analysis to characterize gene expression profiles in a series of intraductal papillary-mucinous tumors (IPMTs) of the pancreas, which represents one of the alternative routes of intraepithelial progression to full malignancy in the pancreatic duct system. Using a cDNA microarray containing 4992 human genes, we screened a total of 13 IPMTs including nine noninvasive and four invasive cases. Expression change in more than half of the tumors was observed for 120 genes, ie, 62 up-regulated and 58 down-regulated genes. Some of the up-regulated genes in this study have been previously described in classical pancreatic carcinomas such as lipocalin 2, galectin 3, claudin 4, and cathepsin E. The most highly up-regulated genes in IPMTs corresponded to three members of the trefoil factor family (TFF1, TFF2, and TFF3). Immunohistochemistry performed on five genes found to be differentially expressed at the RNA level (TFF1, TFF2, TFF3, lipocalin 2, and galectin 3) showed a good concordance between transcript level and protein abundance, except for TFF2. Hierarchical clustering organized the cases according to the dysplastic and invasive phenotype of the IPMTs. This analysis has permitted us to implicate several genes (caveolin 1, glypican 1, growth arrestspecific 6 protein, cysteine-rich angiogenic inducer 61) in tumor progression. The observation that several genes are differentially expressed both in IPMTs and pancreatic carcinomas suggests that they may be involved at an early stage of pancreatic carcinogenesis. (Am J Pathol 2002, 160:1745-1754) Intraductal papillary-mucinous tumors (IPMTs) are a distinct form of exocrine pancreatic neoplasm characterized by dilated ducts that are lined by a proliferation of papillary mucinous epithelium. 1-3 Although IPMTs usually show a favorable outcome compared with classical ductal pancreatic adenocarcinomas, all gradations from lowand high-grade dysplasia through to invasive carcinoma may be encountered. This uncommon type of pancreatic tumor represents a clinically detectable model of intraepithelial neoplasia.Whereas considerable insights into the genetic basis of classical ductal pancreatic adenocarcinoma have been generated, less is known about the genetic alterations in progenitor lesions. 4 -6 Since a progressive accumulation of genetic alterations is now widely accepted for the development of tumors, the identification of the molecular events involved in each step of tumor progression is essential in understanding pancreatic carcinogenesis. Various factors account for our knowledge in this field being less advanced than for tumors in other organs such as colorectal adenoma/carcinoma. In contrast to colonic adenomas, the pancreatic pre-neoplastic lesions are almost always discovered microscopically only after fixation, are relatively inaccessible to biopsy and below the resolution of current imaging modalities. Such les...