Defeat Deficiency: What Nutrients are Lacking in the Gluten-Free Diet?

The glow has dimmed on the gluten-free halo. The diet is no panacea, no formula for peak performance.

“A gluten-free cookie or a brownie is no more nutritious than a regular brownie or cookie or cake made with gluten,” says Shelley Case, RD, of Calgary, Canada, author of Gluten Free: The Definitive Resource Guide. “There’s nothing magical about going gluten free.”

However, for people with celiac disease, it is the only treatment available. Having removed all sources of gluten from their diet, they must also achieve good nutrition. As with any diet, convenience foods may not be the healthiest choices.

“Every time you go on a restrictive diet, there is a risk for nutritional deficiency,” says Jocelyn Silvester, MD, instructor of pediatrics at Harvard Medical School in Boston. “While treating celiac disease helps you absorb nutrients better, it might also put you at risk for not absorbing the right profile of nutrients.”

Medical literature contains little data about long-term nutrition of patients on a gluten-free diet. The Manitoba celiac cohort study is following a group two years after diagnosis to see how treatment affects their nutrition. Silvester, who completed her residency training at University of Manitoba in Winnipeg, Canada, maintains ties with this research. She hopes it will show whether patients normally achieve good nutrition or need more follow-up. So what’s lacking when it comes to nutrients in the gluten-free diet? Read on for more on missing nutrients and what steps to take when going gluten free. 


Malabsorption and the Gluten-Free Diet 

The first hurdle for new patients is avoiding gluten so they can heal. Celiac flattens the villi, small, finger-like projections lining the small intestine. Damaged villi have less surface area and absorb fewer nutrients. If children do not get enough calories, they may fail to thrive or have delayed growth. Adults can suffer unwanted weight loss.

“Oftentimes, kids will adapt to this by increasing their caloric density to try to keep their weight stable. Once the gut heals, that higher caloric diet is suddenly too much for them,” says Hilary Jericho, MD, director of pediatric clinical research at University of Chicago Celiac Disease Center.

Adopting a new mindset that they do not need to consume 3,000 calories a day can be a big adjustment along with many other changes during childhood.


Malabsorption can cause specific nutrient deficiencies. Silvester says, “Nutrients that are absorbed in the first part of the duodenum—iron and calcium—are two of the main nutrients we see difficulties with.”

Iron and the Gluten-Free Diet 

Iron maintains a healthy red blood supply and stores oxygen in the muscles. Iron-deficiency anemia is common in new patients and often alerts doctors that a patient might have celiac. Fatigue, weakness and dizziness are common symptoms.

Adopting a gluten-free diet should be the first step to address iron deficiency, says Case. When the villi heal, they should absorb nutrients normally again.

Jericho says, “If you are having ongoing iron deficiency problems, then we really need to look into this and understand why. Once the gut is fully healed, you should not run into that problem.”


Case adds that iron supplements can be hard on the stomach, often problematic for people recovering from celiac.

She advises that the human body absorbs iron most readily from meat, fish and shellfish. The form of iron occurring in plants is less easily absorbed. Plant foods rich in iron include beans, peas, lentils, tofu, quinoa, seeds and eggs. The gut absorbs iron from plants better if they are eaten alongside meats or vitamin C foods like citrus fruit, strawberries, cantaloupe, peppers, tomatoes and potatoes.

Vitamin D, calcium and the Gluten-Free Diet 

Malabsorption can affect calcium and vitamin D. Both nutrients support healthy bones. Calcium in the bones alone contributes up to 2% of body weight. Children need a lot of it to grow and lay down critical bone mass.

“Adolescence and early 20s is a peak age when bone mineral density is accrued,” says Silvester. “Then, like so many other things in life, it’s a downhill slope from there. It’s really important to get kids better and make sure they’re getting adequate calcium and vitamin D so they can start with normal stores. If they start with a lower bone mass, then they are at greater risk of developing osteoporosis later in life.”


Calcium is also necessary for functions of the muscles, nerves, heart and other systems. If the body lacks enough for these vital tasks, it extracts calcium from the bones. Calcium deficiency can cause osteopenia, a thinning of the bones, or osteoporosis, making the bones more porous and fragile.

The prevalence of bone disease in celiac is unclear. However, patients face a greater risk of bone fracture. Experts consider poor bone density one of the potentially serious effects of untreated celiac.

Adding to the problem, damaged villi produce less lactase enzyme to digest lactose. Before being diagnosed with celiac, many patients compensate for lactose intolerance by restricting their milk consumption. This could potentially increase risk for bone disease, says Silvester.


Sometimes new celiac patients need a temporary lactose-free diet, says Case. Once the villi heal, they begin producing lactase enzyme normally. Then dairy products can be reintroduced to the diet. Intestinal healing also restores normal absorption of calcium and vitamin D.

Bone mass is difficult to improve in adulthood, Silvester says, “There is some interesting recent data from people diagnosed with celiac disease in adulthood that suggests that they might be able to recover their bone mass when they start a gluten-free diet.”

Exposure to sunlight provides the most important natural source of vitamin D. However, people in the northern states and Canada don’t get enough and need more from fortified food or supplements.

Milk, cheese and yogurt are the best dietary sources of calcium. Leafy green vegetables, seafood, nuts and dried beans offer smaller amounts.


Dairy products, cereals, juices and some other foods may be fortified with vitamin D depending on the producer in the United States. In Canada, vitamin D fortification is mandatory for milk and margarine. Fortified foods can also provide vital calcium.

Fiber and the Gluten-Free Diet 

Once the body heals, it needs the right profile of macronutrients: protein, carbohydrates and fat. Here convenience foods often fall short. For example, many gluten-free breads rely heavily on starch and fat to compensate for the missing textural properties of gluten.

Fiber is often overlooked. Case says it used to be assumed everyone with celiac had diarrhea, so no one considered adding fiber to the diet. However, one-third of celiac patients now present with constipation.

“If they already were constipated and then you remove your whole grains and wheat bran and all those high-fiber foods because they’re full of gluten, now we’ve got even more problems. All the more reason why we need to focus on fiber-rich foods,” says Case.


She advises checking nutritional information to compare products and see which contain more fiber. Whole fruits, vegetables, pulses (part of the legume family), nuts and seeds are naturally good sources of fiber. With oats and pulses like dried beans, peas and lentils, it is critical to look for a gluten-free label because they are subject to cross-contamination from wheat.

“I’m delighted to see a lot more pulse-based pastas coming on the market, such as lentils and chickpeas,” Case adds. “Traditional gluten-free pastas are usually made with white rice flour, corn flour and maybe quinoa. If you look at the label, again, they’re not enriched with iron and B vitamins like wheat-based pasta, and they don’t tend to have a lot of fiber. If you can switch to a pulse-based pasta, you get a lot more fiber and protein and more satiety.”

Convenience Foods and the Gluten-Free Diet 

“Convenience foods tend to be higher in sugar and fat and have less vitamins and nutrients than if you’re eating non-processed foods,” says Silvester. “Previously, going gluten free often meant cooking a lot of food for yourself. People would often substitute in more healthy foods, more whole foods, more fruits and vegetables. Now it’s easier to follow a low-quality gluten-free diet than ever before. It’s not enough to just be gluten free. You have to make sure that they’re eating a balanced, healthy gluten-free diet.”


To investigate the effect of gluten-free products, Jericho’s research team compared patient records before and after 2011, when gluten-free products became widely available. Specifically, they looked at how quickly body weight increased after diagnosis and treatment. The new study in Journal of Pediatric Gastroenterology and Nutrition found no significant change overall due to small sample size. However, adolescents showed a tendency toward higher body mass index after 2011.

In follow-up phone surveys, her team asked the teen patients now in their 20s to recall their eating habits at the time. All respondents diagnosed after 2011 said they consumed processed gluten-free foods sometimes or all of the time. One reported never eating processed foods before 2011 but admitted to always using them after they became available in stores. Besides the products being convenient and easy to prepare, patients reported it helped them fit in with their friends.

If further research shows an impact on adolescents, Jericho suggests they would benefit from a refresher nutrition course two years after diagnosis. It will affect their health down the road.

As a consulting dietitian, Case often receives products from companies. Her responsibility is to make sure they are safe, and the gluten-free claim is valid: “But then I look at the nutrition facts and have to say, ‘Is this product really all that great, or would I be better to eat something else, like some fruit, nuts and seeds or a trail mix, rather than these gluten-free cookies?’”

Case is not against eating treats: “Remember, we all like to celebrate birthday parties and special occasions. Children like to have a treat with their friends. Just be aware that some foods can be a lot more nutritious.”

See a dietitian

Case emphasizes, “It’s critical to work with a registered dietitian with expertise in celiac to individualize the treatment. Everybody has different issues going on, likes and dislikes, their lifestyle, what their cooking ability is or access to different foods. These are all things that the dietitian will go through.”

Case encourages people on the diet to watch for and consider using brands that enrich their products. Only a few do so now.

Silvester says folate deficiency in the North American diet has been addressed with fortification of grain products. Many gluten-free products don’t have folate added, so this especially can be a problem for patients with celiac.

“Patients with CD are going back to the pre-supplementation era,” says Silvester, but adds, “One of the great things about the body is it’s very good at absorbing what it needs and can scavenge minimal amounts from the diet to have adequate amounts in the body.”

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