The beneficial effects of dietary FO with respect to autoimmune disease, CVD and some types of cancer are well established. Studies conducted over the last 10-15 years have established the potent effects of FO on gene expression in the previously mentioned diseases. The effects of dietary FO appear to be selective in nature, with the expression of individual genes simultaneously being increased, decreased or completely unaffected. In order to elucidate the molecular mechanism(s) involved, recent studies have focused on analysing the effects of the long-chain polyunsaturated n-3 fatty acids EPA and DHA which are highly enriched in FO and thought to be the primary mediators of its biological activity. Indeed, it has been found that EPA and DHA appear to both directly and indirectly modulate gene expression in vivo, depending on the gene examined. The direct effects of EPA and DHA are most probably mediated by their ability to bind to positive and/or negative regulatory transcription factors, while the indirect effects appear to be mediated through alterations in the generation of intracellular lipid second messengers (e.g. diacylglycerol and ceramide). Future studies need to be focused on further elucidation of the inter- and intracellular signalling events mediated by dietary n-3 fatty acids. Understanding the molecular mechanism(s) modified by dietary FO will ultimately lead to improved dietary strategies to aid in the prevention of autoimmune disease, CVD and/or certain types of cancer.