The epidemiological association between high intakes of n-3 fatty acids (FA) and decreased morbidity and mortality from cardiovascular disease (CVD) can be explained by two main basic mechanisms: (a) an effect on atherothrombosis, and (b) an effect on cardiac arrhythmias. These mechanisms probably reflect different beneficial influences of n-3 FA on cardiovascular biology. Effects on atherothrombosis include the modulation of the expression of pro-atherogenic genes (e.g., endothelial leukocyte adhesion molecules, inflammatory cytokines and cyclooxygenase (COX)-2) and the hepatic synthesis of very low density lipoproteins (VLDL), and are slow in onset, requiring incorporation into cell membrane phospholipids, and usually doses in humans in the order of 3g/day or higher. Effects on cardiac arrhythmias include complex interactions with ion channels (sodium, potassium and calcium channels), typically requiring the presence of free FA in extracellular fluids and usually occurring with lower doses (around 1g/day) of nutritional or pharmacological intake. We have focused most of our research effort in unraveling the pathophysiological background of protection by n-3 FA from atherothrombosis. As the result of incorporation of n-3 FA in the sn-2 position predominantly of the phosphatidyl ethanolamine pool in the inner leaflet of the plasma membrane, n-3 FA appear on the one hand to increase the production of bioactive lipid mediators (protectins and resolvins) affecting cytokine-induced signal transduction; and on the other hand to directly interfere with the generation of reactive oxygen species (mostly hydrogen peroxide), directly responsible for the activation of the transcription factor nuclear factor (NF)-kappaB, which controls the expression of a variety of pro-inflammatory and pro-atherogenic genes, including those encoding for interleukin (IL)-1, IL-6, IL-8, tumor necrosis factor (TNF)alpha, vascular cell adhesion molecule-1 (VCAM-1), E-selectin, and COX-2. The upstream-direct or indirect-inhibition of cytokine- and other atherogenic trigger-induced signaling pathway may involve interference with the activation of protein kinase (PK) C isoforms and NADP(H) oxidase. Such interference may also explain the blunt anti-inflammatory effect of n-3 FA in many experimental models and clinical conditions of inflammation. All together, these mechanisms may provide an integrated view of how n-3 FA may affect CVD.