Posted on: March 7, 2016 at 8:53 am
Last updated: September 22, 2017 at 1:47 pm

What is malabsorption?

There is an impressive cascade of events that happens from the moment food touches the tongue. We’ll start to secrete saliva, which will lubricate our food as it travels down our esophagus and provide enzymes to help break our food down. This reaction triggers stomach acid production, which then triggers pancreatic enzymes as well as bile production from the liver to further breakdown and transport our food. The food is sent through the small intestine to the large intestine, where we absorb most of its nutrients.

Malabsorption is the reduced ability to absorb nutrients from the foods that you’re eating. There are numerous symptoms and causes of malabsorption, but it is usually a result of maldigestion. Maldigestion is the reduced ability to break food down properly.

General malabsorption symptoms include:

  •  Abdominal bloating
  •  Mucous in the stool
  •  Diarrhea
  •  Greasy stools
  •  Undigested food in the stool
  •  Fatigue
  •  Stinky stools
  •  Nutrient deficiencies
  •  Fatigue or lethargy
  •  Muscle wasting
  •  Weight loss

Causes of malabsorption:


There are numerous causes of malabsorption. Some causes are due to our body’s inability to process specific ingredients, such as in celiac disease, lactose intolerance and disaccharide intolerance. Other causes could be due to an issue with the structural integrity of the intestinal lining, such as Crohn’s disease and ulcerative colitis. Functional causes of malabsorption are much more common and will be discussed in more detail in this article.

There are so many aspects of our society that work to throw off the complicated process of digestion. One of the most common issues is that we end up with limited stomach acid production. If we do not produce enough stomach acid, we won’t break food down properly and it will enter our small intestine undigested. Once this happens there is virtually no way we can extract nutrients from it and it will begin to ferment and cause inflammation in our intestine. This is usually the mechanism behind irritable bowel syndrome (IBS). Our bodies produce inflammation around any foreign bodies that come into contact with our mucosa (internal lining). If food is undigested, our small intestine views it as a foreign body. The combo of fermentation and inflammation causes bloating, smelly gas, abdominal pain, cramping, diarrhea and mucous in the stool.

Can you eat chocolate on the Keto diet? Good news!

Download our free report today for instant access to 28 recipes for making delicious chocolate treats — all 100% Keto approved.


10 Factors which prevent stomach acid production:

  1. Eating on the go
  2. Consuming caffeine
  3. Physical stress
  4. Mental stress
  5. Emotional stress
  6. Leaving too much time between meals
  7. Acid blocker medications (commonly prescribed for acid reflux)
  8. Black tea, black coffee, over-steeped green tea
  9. Hypothyroidism
  10. Hyperthyroidism

The first 6 factors cause us to secrete too much cortisol, our main stress hormone. If we’re secreting a stress hormone, our brain thinks we’re in fight or flight mode. We can’t be in this state as well as ‘rest and digest’ mode at the same time. If we’re constantly in this state of stress our stomach isn’t producing enough stomach acid and food is being passed into our small intestine only partially broken down. Because it’s not broken down into simple enough pieces we can’t absorb nutrients from it and we create inflammation to try to remove it.

(If you’re wondering why leaving too much time between meals has an effect on this, you should know that hypoglycemia, or low blood sugar, causes us to secrete cortisol. That means if it’s been more than 3 or 4 hours since you ate you’re most likely secreting the same hormone you secrete when you’re on a hike and you see a bear.)


Taking acid blockers will prevent you from producing stomach acid which leads to multiple nutrient deficiencies if taken long-term. I call these medications “anti-multivitamins”. In practice it is super common to have patients who have been on acid blockers for years and develop iron deficiency anemia, B12 deficiency, osteoporosis, and magnesium deficiency.

Black tea, black coffee and over-steeped green tea contain tannins (the same chemical used to turn cowhides into leather!). Constant exposure to tannins will prevent absorption of nutrients. Patients with Hemochromatosis (iron overload) are usually recommended to consume black coffee and black tea liberally to prevent iron absorption. I suspect overconsumption of black coffee and black tea are why so many elderly patients have nutrient deficiencies. Older folks tend to not consume nutrient-dense food and drink way too much black coffee or tea.

Hypothyroidism will decrease stomach acid levels since it slows down your entire metabolism, and hyperthyroidism will decrease stomach acid levels since it puts the body into fight or flight mode constantly.

Blood tests which can indicate malabsorption:

The best, and most accurate blood tests are Ferritin (iron storage), B12 and Complete Blood Count (CBC). The reference ranges of these tests are a bit too broad so it is important to get someone who can look at blood work functionally to review this blood work. Most other nutrients are not very accurately tested in the blood since they concentrate in other tissues. These nutrients may be difficult to test but a Naturopathic Doctor might be able to identify what you are deficient in based on your symptoms and your diet.


Common signs of nutrient deficiencies Common deficient nutrients:

Malabsorption may result in several nutrient deficiencies. These can range in severity based on intake of the nutrients and how severe malabsorption is. For instance, if someone has a great diet, has a lactose intolerance but only consumes dairy once a month they most likely won’t have a nutrient deficiency. On the other hand, if someone has a poor diet, just depends on carbohydrates and they have celiac disease, they’re most likely going to get osteoporosis fairly early, along with a plethora of other symptoms due to a broad range of nutrient deficiencies. Here are some common signs of nutrient deficiencies, along with the most common deficiencies which cause them:

  • White spots on nails: Zinc
  • High blood pressure: Magnesium, Calcium, Potassium
  • Muscle twitches: Magnesium, Calcium, Sodium
  • Fatigue:  Iron, B12, Iodine
  • Pale fingernail beds: Iron
  • Restless leg syndrome: Magnesium, Iron, Calcium
  • Hair loss:  Protein, Biotin (B7), Iron
  • Palpitations or irregular heart rhythm: Magnesium, Potassium, Calcium
  • Brittle nails:  Zinc, Calcium, B7, Protein, Iron, Silica
  • Weight loss: Protein, Fat, Carnitine
  • Weight gain: Chromium, Iodine
  • Hypothyroidism or enlarged thyroid: Iodine, Tyrosine, Selenium
  • Amenorrhea (no period):Iron, Fat, Protein
  • Pilaris keratosis (chicken skin on arms and legs): Vitamin A
  • Weak immune system: Vitamin D, Zinc, Vitamin C
  • Bleeding gums: Vitamin C
  • Numbness and tingling:  B12, Calcium
  • Osteoporosis:  Calcium, Phosphorous, Protein, Vitamin D,
  • High blood sugar:  Manganese, Chromium, Manganese



Dr. Justin Gallant
Naturopathic Doctor
Contributor to The Hearty Soul.

A quick note from our founders

Can you eat chocolate on the Keto diet? Good news!

Now you can thanks to our brand new free report "Keto Chocolate Treats."

Download this free report today for instant access to 28 recipes for making delicious chocolate treats — all 100% Keto approved.

You won't be disappointed!

Get your copy of Keto Chocolate
Treats now (free)