The association of high plasma cholesterol levels with the development of atherosclerosis is well known. The metabolic pathways that are regulated by cholesterol and the mechanisms involved are less well understood. Recent studies have identified not only cholesterol, but also oxysterols and isoprenoids, derived from the cholesterol biosynthetic pathway, as new signaling molecules. The transcriptional and post-transcriptional regulation of specific genes and metabolic pathways by these newly discovered signaling molecules may be important in the development of human disease and forms the topic of this review.