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There is marked heterogeneity in the clinical response to omega-3 fatty acid therapy with many authors documenting futility in large-scale trials, secondary re-analysis, and meta-analysis. The question of failure in the context of omega-3 therapy is multifactorial and complicated by the observation that fish intake has been broadly linked to significant risk reductions across a range of conditions. The question that remains is how can we resolve the discrepancy between pre-clinical evidence and epidemiology, which dually emphasize the benefit of omega-3 therapy against the limited success of large-scale clinical trials and smaller scale clinical studies that do not consistently report benefit and may even report harm, especially as it pertains to atrial fibrillation. We present three primary considerations that may clarify the supposed failures of omega-3 therapy: 1) correction for omega-3:omega-6 ratio and competition, 2) variation in the fatty acid composition and quality of omega-3 products, and 3) fundamental concerns pertaining to the omega-3 vehicle and its impact on omega-3 metabolism. While the predominant source of omega-3 therapy is supplements, they are typically not regulated prior to market like drugs and have significant variability in fatty acid composition, vehicle, oxidation, and quality control. Further, the individual response to omega-3 therapy is likely variable and dependent on ambient dietary conditions and inherited differences in endogenous desaturase activity, which has infrequently been accounted for in large studies. The net effect of these concerns should engender pharmaceutical and consumer companies alike to consider 1) refining trial design and 2) consider the role of oxidation in the failure of omega-3 products.