Cyclooxygenase 2 (COX-2) overexpression has been described in sporadic colonic neoplasia, but its role in ulcerative colitis (UC) neoplastic progression remains unexplored. Although the specific role of cyclooxygenase in colonic neoplasia is uncertain, its inhibition by nonsteroidal anti-inflammatory drugs decreases the risk of sporadic colonic adenocarcinoma and causes regression of adenomas in familial adenomatous polyposis. To investigate the role of COX-2 in UC-associated neoplasia, we assessed COX-2 protein and mRNA expression throughout the spectrum of UC-associated neoplastic lesions in four total colectomy specimens, using immunocytochemistry and a novel TaqMan reverse transcriptase-polymerase chain reaction assay. The findings were correlated with DNA ploidy and inflammatory activity. We found COX-2 overexpression throughout the neoplastic spectrum in UC (P < 0.0001, R 2 ,)35.0؍ even in diploid samples that were negative for dysplasia. Overall, neoplastic change explained 53% of the variation in COX-2 expression, whereas inflammatory activity explained only 11%. COX-2 was overexpressed in all aneuploid samples and in 38% of diploid samples (P ؍ 0.0074). cDNA representational difference analysis was also performed and revealed that COX-2 mRNA was an up-regulated cDNA representational difference analysis difference product. COX-2 overexpression occurs early in UC-associated neoplasia, and the increase cannot be explained by inflammatory activity alone. The data suggest that COX-2-specific inhibitors may have a chemopreventative role in UC but the possibility that they could exacerbate UC inflammatory activity needs to be tested. Cyclooxygenase 1 (COX-1) and cyclooxygenase 2 (COX-2) are cyclooxygenase enzymes that convert arachidonic acid to inflammatory and other physiological mediators, including prostaglandins, prostacyclin, and thromboxane. 1,2 COX-1 is constitutively expressed in most tissues, including the gastrointestinal tract, at a relatively stable level and is thought to help protect the gastrointestinal tract from injury. 1,2 COX-2 is an inducible cyclooxygenase whose production is stimulated by interleukin-1, tumor necrosis factor, and many other mediators. 1,2 COX-2 is thought to play a role in the reparative process after mucosal injury in the gastrointestinal tract. 1,2 Multiple studies suggest that COX-2 plays a role in sporadic colorectal neoplasia, based on its overexpression in colonic adenomas and carcinomas, as shown by both immunohistochemistry and reverse transcriptasepolymerase chain reaction (RT-PCR). [3][4][5] Cyclooxygenase inhibitors such as nonsteroidal anti-inflammatory drugs (NSAIDs) substantially decrease the risk of colorectal cancer, as well as the number and size of adenomas in familial adenomatous polyposis patients. 6 -8 Experimentally, NSAIDs prevent colonic adenocarcinoma in rodents with an familial adenomatous polyposis phenotype (the APC min mouse model). 9,10 Understanding the role of COX-2 in colonic neoplasia is thus particularly important because of these t...