The effect of nutrients on gene expression is an area of considerable interest as the number of genes coding for key regulatory proteins in metabolic pathways is investigated. This paper presents an overview of the role of omega-6 and omega-3 fatty acids on the expression of genes involved in lipogenesis, glycolysis, glucose transporters, inflammation, early gene expression, and vascular cell adhesion molecules. Whereas some of the transcriptional effects of omega-6 and omega-3 fatty acids appear to be mediated by eicosanoids, the suppression of lipogenic and glycolytic genes is independent of eicosanoid synthesis, and appears to involve a nuclear mechanism directly modified by these fatty acids.