The PUFAs, once absorbed in the intestines, are then transported, via the bloodstream, to all tissues. Hundreds of small molecules have been identified as metabolites of these few omega-3 and omega-6 precursors in human tissue. Yet, it is the overall balance between omega-3s and omega-6s that seems to modulate many biological processes including the relaxation and contraction of smooth muscle tissue, blood coagulation, and – significantly – inflammation. Although much research demonstrates a potentially important relationship between PUFA intake and the risk of disease, it remains challenging in current dietary intervention studies to accurately evaluate the impact of increased intake of omega-3s by food or supplementation. A frequently confounding factor is the variability inherent in studies of control diets. A different nutritional value may accompany such diets compared with a diet enriched in omega-3– a different composition of fatty acids, for example. Other frequent issues relate to the chemical nature, source, and dose of the omega-3 used in the dietary intervention studies. These issues include the mixed use of the different types of omega-3s, such as EPA and DHA, or the different forms of omega3s, such as triacylglycerols, phospholipids, or ethyl esters. Furthermore, dietary intervention studies in humans are often associated with high individual genetic and environmental variability. All of these factors militate against an accurate evaluation of the biological effects of omega-3s, and no molecular markers of omega-3 intake currently exist. In 2004, the fat-1 transgenic mouse model was developed to eliminate many of the confounders inherent in omega-6/omega-3 research. The mouse was engineered to carry the C. elegans fat1 gene, which can add a double bond into an unsaturated fattyacid hydrocarbon chain, thus converting omega-6 to omega-3 fatty acids. Though the mice are not exposed to an omega-3 diet, this conversion results in an abundance of omega-3 and a reduction in omega-6 fatty acids in their organs. The resulting omega-6/omega-3 fatty acid profile has also been shown to be comparable to those obtained by dietary supplementation. The animals therefore provide a controlled approach for evaluating the effects of a balanced omega-6/omega-3 ratio, one that does not introduce the confounding factors that result from enforcing different test diets. To date, the fat-1 transgenic mouse model has been widely used, and has demonstrated that balancing the omega-6/omega-3 ratio can protect against a wide variety of diseases, including chronic inflammatory diseases and cancer. However, the molecular mechanisms underlying these beneficial effects remain to be fully elucidated. In the present study, we used a multi-platform lipidomic approach to compare the molecular phenotype of fat-1 and WT mice exposed for six months to an identical high-omega-6.