The takeaway: The pros and cons of anti-nutrients on long-term human health is an area of active research. Though certain foods may contain residual amounts of anti-nutrients after processing and cooking, the health benefits of eating these foods outweigh any potential negative nutritional effects. Eating a variety of nutritious foods daily and avoiding eating large amounts of a single food at one meal can help to offset minor losses in nutrient absorption caused by anti-nutrients.
The term “anti-nutrients” suggests what they are. Whereas nutrients are substances that nourish plants and animals to grow and live, anti-nutrients earn their title because they can block the absorption of nutrients. Anti-nutrients are naturally found in animals and many plant-based foods. In plants, they are compounds designed to protect from bacterial infections and being eaten by insects. 
There are several compounds in the foods we eat classified as anti-nutrients. Examples include:
- Glucosinolates in cruciferous vegetables (broccoli, Brussels sprouts, cabbage)—can prevent the absorption of iodine, which may then interfere with thyroid function and cause goiter. Those already with an iodine deficiency or a condition called hypothyroidism are most susceptible.
- Lectins in legumes (beans, peanuts, soybeans), whole grains—can interfere with the absorption of calcium, iron, phosphorus, and zinc.
- Oxalates in green leafy vegetables, tea—can bind to calcium and prevent it from being absorbed.
- Phytates (phytic acid) in whole grains, seeds, legumes, some nuts—can decrease the absorption of iron, zinc, magnesium, and calcium. [2,3]
- Saponins in legumes, whole grains—can interfere with normal nutrient absorption.
- Tannins in tea, coffee, legumes—can decrease iron absorption.
It is not known how much nutrient loss occurs in our diets because of anti-nutrients, and the effects vary among individuals based on their metabolism and how the food is cooked and prepared. Many anti-nutrients like phytates, lectins, and glucosinolates can be removed or deactivated by soaking, sprouting, or boiling the food before eating.
Another consideration is that these anti-nutrients affect the absorption of nutrients eaten at the same meal. Therefore to lower this risk, it is recommended to avoid eating large quantities of foods containing anti-nutrients at one meal, and to eat a balanced diet throughout the day with a variety of foods.  For example, instead of eating two cups of bran cereal with milk for breakfast, choose one cup of cereal with milk and one cup of fresh berries.
People who are at high risk for diseases related to mineral deficiencies, such as osteoporosis with calcium deficiency or anemia with iron deficiency, may wish to monitor their food choices for anti-nutrient content. Another strategy could be to alter the timing of eating foods with anti-nutrients. Examples are to drink tea between meals instead of with a meal to reduce the chances of iron being poorly absorbed, or taking a calcium supplement a few hours after eating a high-fiber wheat bran cereal that contains phytates.
Studies on vegetarians who eat diets high in plant foods containing anti-nutrients do not generally show deficiencies in iron and zinc, so the body may be adapting to the presence of anti-nutrients by increasing the absorption of these minerals in the gut. 
Keep in mind that anti-nutrients may also exert health benefits. Phytates, for example, have been found to lower cholesterol, slow digestion, and prevent sharp rises in blood sugar.  Many anti-nutrients have antioxidant and anticancer actions, so avoiding them entirely is not recommended. [3,4]
Keeping an eye on glucosinolates
A few studies have found a small but significant increased risk of disease with higher intakes of glucosinolates, which are obtained mainly through cruciferous vegetables. In two studies following three large prospective cohorts of 42,170 male and 168,404 female health professionals for several years, a higher intake of glucosinolates was associated with a slightly higher risk of heart disease and type 2 diabetes in men and women. Individuals with the highest intakes of glucosinolates had a 19% increased risk of type 2 diabetes compared with those with the lowest intakes, even after adjusting for other factors that can affect diabetes, such as BMI, physical activity, and smoking.  The strongest associations were observed for Brussels sprouts when comparing the highest (1 or more servings/week) and lowest intakes (never or almost never). In a separate analysis of these same three cohorts looking at intakes of glucosinolates and heart disease, participants who consumed one or more servings a week of Brussels sprouts and cabbage had a higher heart disease risk than those who consumed these vegetables less than once per month.  The authors did not recommend avoiding these foods but rather emphasized a need for more studies to replicate and confirm these findings to better understand this possible relation, as several other studies have shown a protective effect on diabetes and heart disease with higher intakes of cruciferous vegetables.