It has been suggested that the potential antithrombotic effect of fish oils may theoretically increase the risk for bleeding, which may be a safety concern for individual patients. However, clinical trial evidence has not supported increased bleeding with omega-3 fatty acid intake, even when combined with other agents that might also increase bleeding (such as aspirin and warfarin). Another potential safety concern is the susceptibility of omega-3 fatty acid preparations to undergo oxidation, which contributes to patient intolerance and potential toxicity. Finally, large amounts of fish consumption may result in adverse experiences due to the potential presence of environmental toxins such as mercury, polychlorinated biphenyls, dioxins, and other contaminants. The risks of exposure to environmental toxins and hypervitaminosis with fish consumption are substantially reduced through purification processes used to develop selected concentrated fish oil supplements and prescription preparations.

Thus, in choosing which fish oil therapies to recommend, clinicians should be aware of available information to best assess their relative safety, which includes the US Food and Drug Administration (FDA) and Environmental Protection Agency (EPA) advisory statement regarding fish consumption, the meaning of certain labeling (such as "verification" through the US Pharmacopeia) and the differences in FDA regulatory requirements between nonprescription fish oil supplements and prescription fish oil preparations, and how all of this is important to the optimal treatment of patients.