Flaxseed oil and fish oil both contain omega-3 fatty acids, which serve a number of purposes in the human body. Omega-3 fatty acids, also called polyunsaturated fats, or PUFAs, can reduce the risk of heart disease and improve a number of other conditions. Like all supplements, flaxseed and fish oils also have risks; always discuss them with your medical practitioner before taking them.
Definition
The omega-3 fatty acid in flaxseed is alpha-linolenic acid, also called ALA, while fish oil contains two omega-3 fatty acids, eicosapentaenoic acid, or EPA, and docosahexaenoic acid, or DHA. In the body, ALA breaks down into DHA and EPA.
Breakdown
Alpha-linolenic acid converts incompletely to DHA and EPA in the body; in healthy young men, around 8 percent of ALA converts to EPA and between 0 to 4 percent converts to DHA. Healthy young women convert ALA more efficiently, possibly because of the effects of estrogen. Around 21 percent of ALA converts to EPA and 9 percent to DHA.
Benefits
While both flaxseed oil and fish oil have benefits, DHA and EPA appear to have the most protective benefit in heart disease and lowering lipid levels. DHA may also improve blood pressure levels slightly, with decreases of 2 to 5mmHg reported, with higher doses causing larger drops, MayoClinic.com states. For people with low blood pressure this could cause hypotension and feeling faint. Fish oils appear to lower triglyceride levels, but it's not clear whether ALA has the same effect. Fish oil may also improve arthritis symptoms, but results can take up to three months. DHA may also help improve vision, although studies on this benefit are still ongoing.
Negative Effects
Flaxseed can cause diarrhea or loose stools, and has caused allergic reactions, including anaphylaxis. Fish oil can cause a fishy taste during burping and can also cause heartburn, abdominal pain or diarrhea. Fish oil can enhance the effects of blood thinners, resulting in increased bleeding times or spontaneous bleeding in people taking anticoagulants or in those with a disease that affects blood clotting. Doses of fish oil up to 3g per day are generally regarded as safe and unlikely to cause serious bleeding side effects, according to the Linus Pauling Institute at Oregon State University. Fish oil may also cause a small increase in fasting blood glucose levels. Although usually associated with improved cholesterol levels, fish oil can also increase low-density lipoprotein, the "bad": cholesterol, by 5 to 10 percent in some cases.
Considerations
If you want the benefits of reduced lipid levels and decreased risk of heart disease, choose fish oil supplements over flaxseed, because most of the benefits appear to be related to DHA or EPA. Fish oil, however, may contain methylmercury and contaminants found in fish, although the risk is probably small, MayoClinic.com reports.



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