Flaxseed oil toxicity has not been reported. However, there is conflicting information about the effect of flaxseed oil and one of its major constituents, ALA, on cancer risk.

While most test tube and animal studies suggest a possible protective role for ALA against breast cancer,^{4, 5, 6, 7, 8} one animal study⁹ and a preliminary human study¹⁰ suggested increased breast cancer risk from high dietary ALA. Another preliminary human study reported that higher breast tissue levels of ALA are associated with less advanced breast cancer at the time of diagnosis.¹¹ For prostate cancer, a test tube study reported ALA promoted cancer cell growth,¹² but preliminary human studies have shown ALA to be associated with either an increased^{13, 14} or decreased risk,¹⁵ or no change¹⁶ at all.

Advocates of flaxseed oil speculate that a potential association between ALA and cancer may be due to the fact that meat contains ALA, thus implicating ALA when the real culprits are probably other components of meat. In some studies, however, saturated fat (and therefore probably meat) were taken into consideration, and ALA still correlated with increased risk. The associations between ALA and cancer might eventually be shown to be caused by substances found in foods rich in ALA rather than by ALA itself. However, ALA has been reported to become mutagenic (able to cause precancerous changes) when heated,¹⁷ which concerns some doctors.

The effect of ALA as an isolated substance, and of flaxseed oil on the risk of cancer in humans remains unclear, with most animal and test tube studies suggesting protection, and some preliminary human trials suggesting cause for concern. It is premature to suggest that ALA and flaxseed oil will either cause or protect against human cancer at this time.

Flaxseed oil is not suitable for cooking and should be stored in an opaque, airtight container in the refrigerator or freezer. If the oil has a noticeable odor it is probably rancid and should be discarded.

As with any source of fiber, flaxseed should not be taken if there is possibility that the intestines are obstructed. People with scleroderma (systemic sclerosis) should consult a doctor before using flaxseed. Although a gradual introduction of fiber in the diet may improve bowel symptoms in some cases, there have been several reports of people with scleroderma developing severe constipation and even bowel obstruction requiring hospitalization after fiber supplementation.¹⁸

Animal research suggests that large amounts of flaxseed or lignans consumed during pregnancy might adversely affect the development of the reproductive system.¹⁹ No studies have attempted to investigate whether this could be a problem in humans.

Allergic reactions to flaxseed have occasionally been reported, but are considered very uncommon.^{20, 21}