Flaxseed's most common side effect is gastrointestinal distress, such as bloating and gas. This is because flaxseed contains high levels of fiber. To avoid this, start with a small amount of flaxseed and gradually increase your intake. Another potential side effect is allergic reactions. Some people may be allergic to flaxseed protein or pollen. If you experience any allergy symptoms after consuming flaxseed, stop consumption immediately and see your doctor.