A 4-stage colon simulator and a cell culture-based human intestinal epithelial function model were combined to study the effects of a soluble fiber, polydextrose (PDX), on intestinal microbes and mucosal functions relevant to the risk of colon cancer. We observed sustained degradation of PDX throughout the different stages of the model. The fermentation was characterized by gradual degradation of PDX, production of short-chain fatty acids, and no increasing in putrefactive markers. We observed less marked effects in the microbial densities. When we applied colon fermentation metabolites obtained from the simulators with PDX to Caco-2 colon cancer cell line, a significant dose-dependent decreasing effect on cyclooxygenase-2 (COX-2) and an increasing effect on COX-3 expression levels were observed. PDX concentration appeared not to have effect on the expression levels of COX-1. Overexpression of COX-2 and decreased expression of COX-1 have been suggested to be characteristics of colon cancer. The exact physiological role of COX-3, an intron-retaining splice variant of COX-1, is not known, but it is suspected to play a role in transcriptional regulation of COX-1 and COX-2. In vitro modulation of COX expression by colon microbial fermentation products of polydextrose offers an interesting starting point for further studies on possible risk-decreasing effect of PDX on the development of colon cancer.