Both flaxseed and fish oil contain omega-3 fatty acids that, if consumed regularly, have been linked to a decreased risk of cardiovascular disease, stroke and high blood pressure. However, both are also capable of causing potentially severe side effects in certain users. These side effects range from mild digestive problems and allergic reactions to serious instances of internal bleeding and a possible increased risk for certain types of cancer. Consult your physician before using either fish oil or flaxseed on a regular basis.

Flaxseed is the small, reddish brown seed of the flax plant, also known by its scientific name Linum usitatissimum. Fish oil refers to the oils found in certain types of fish, mainly those that contain large amounts of omega-3 polyunsaturated fatty acids. Although one has a plant source and the other an animal source, both flaxseed and fish oil contain a variety of these omega-3 fatty acids, particularly docosahexaenoic acid, eicosapentaenoic acid and alpha-linolenic acid, more commonly known as DHA, EPA and ALA.

According to the Mayo Clinic, Med TV and the World's Healthiest Foods sites, using flaxseed and fish oil can cause a wide range of digestive problems, including nausea, gas, bloating, acid reflux and heartburn, abdominal pain, constipation and diarrhea. The Mayo Clinic reports that, at extremely high doses, fish oil can result in severe diarrhea that may cause dehydration if left untreated. Most of these unpleasant digestive system side effects can be avoided by taking flaxseed and fish oil with regular meals, drinking plenty of water and starting with very small amounts of both before working up to your supplementation goal.

Both flaxseed and fish oil can cause allergic reactions characterized by the sudden onset of an unexplained rash; itchy skin; difficulty breathing and swallowing; a wheezing sound while breathing; swelling in the lips, face or tongue; or general flu-like symptoms accompanied by a fever and body aches. If you experience any of these symptoms while using fish oil or flaxseed, stop using them immediately and seek medical assistance.

A number of medications can react with fish oil or flaxseed, resulting in unwanted side effects or causing the medicine to be much less effective. For fish oil, these medications include blood thinners like warfarin, birth control pills or other estrogen-containing drugs, beta-blocking drugs like carvedilol or propranolol and diruetics. For flaxseed, drugs that can cause interactions include any diabetes medications; any blood thinners, including aspirin; nonsteroidal anti-inflammatory drugs like Celebrex or ibuprofen; and any thrombolytic drugs.

According to Med TV, recent research into the omega-3 fatty acid ALA indicates that increased consumption of ALA may be linked to a higher incidence of prostate cancer. However, the research was conducted on animal products containing high amounts of ALA, not on plant-based compounds like flaxseed that contain large concentrations of ALA so it is not known definitively if regular flaxseed use can contribute to prostate cancer risk.

Using high doses of either flaxseed or fish oil is linked to an increased risk of internal bleeding. If you notice that you bruise abnormally easily; begin to to vomit blood or notice blood in your stool; have sudden changes in your speech or ability to see; or experience unexplained weakness in one of your limbs while using either substance as a dietary supplement, discontinue their use immediately.