It has been suggested that the short-chain fatty acids (SCFAs) produced by anaerobic bacterial intestinal fermentation of soluble fiber may regulate lipid metabolism in intestine, thus reducing plasma cholesterol levels. However, the exact mechanism of action of SCFAs in lowering cholesterol levels is not fully understood. The aims of this study were to test the effects of SCFAs on gene expression in a human enterocyte cell line Caco-2/TC-7 and to validate microarray data by real-time PCR. Human Caco-2/TC-7 enterocytes were cultured on transwell filter inserts and incubated with the SCFAs acetate (Ac), propionate (Pr), and butyrate (Bu). Total RNA was then isolated for microarrays and quantitative real-time PCR analysis. Treatment of human enterocytes with Pr and Bu affects a wide variety of genes. These genes were classified according to the PANTHER classification system, and the results showed that different biological processes and metabolic pathways were modified by Pr and Bu treatment, including the intestinal cholesterol biosynthesis pathway. Differential array expression analysis showed that nine genes were downregulated in this pathway, and these results were validated by real-time PCR. This in vitro study allowed us to identify a wide variety of biological processes and metabolic pathways affected by the SCFAs tested. Importantly, our results show that the global effect of Pr and Bu is to downregulate the expression of nine key genes involved in intestinal cholesterol biosynthesis, thus possibly inhibiting this pathway.