3 Reasons for Vitamin D Malabsorption

This post was originally published in January of 2019 and received some minor updates in June of 2026.

Not only is Vitamin D one of the most powerful factors in taming autoimmunity, it’s also critical for maintaining our overall health and fending off degenerative disease. It helps strengthen muscles, build bones, regulate insulin, and quiet inflammation, to name a few.

As Dr. Greg Plotnikoff says,“Vitamin D replenishment is the single most cost effective thing we can do in modern medicine.” 

A lack of Vitamin D has been shown to play a role in:

  • Osteoporosis
  • Heart disease
  • Diabetes and metabolic syndrome
  • Gout
  • Infertility
  • PMS 
  • Fibromyalgia
  • Alzheimer’s 
  • Arthritis
  • Chronic fatigue syndrome
  • Psoriasis
  • Parkinson’s 
  • Osteoarthritis
  • High blood pressure
  • Depression
  • Breast, prostate, colon and 14 other cancers
  • Hashimoto’s and other autoimmunity *

* To read more about Vitamin D in general and more specifically, the Vitamin D and thyroid health connection, see my post for Dr. Frank Lipman’s blog, The Link Between Vitamin D and Thyroid Health

We only receive about 10 percent of our Vitamin D requirement from our diet because there are so few foods that contain it. Those include egg yolks, fatty wild fish (salmon, mackerel, tuna, herring, halibut, and sardines), shiitake mushrooms, and fortified foods (milk, yogurt, some cereals, and orange juice). 

Sun exposure is your best bet for ensuring sufficient levels…there’s no evidence suggesting that a moderate amount of sun exposure causes skin cancer. Most of us can get our daily dose with just 20 minutes of sun on our face, arms, or legs in the spring, summer, and fall. Fortunately, it’s impossible for your body to generate too much Vitamin D from sunlight exposure alone. Your body will self-regulate.

Many in the functional medicine community state that Vitamin D levels should between 50-80 ng/ml. 

Maximizing Vitamin D absorption and metabolism
A variety of factors can negatively impact our ability to utilize all of that Vitamin D we’re making or supplementing with. (See why I no longer recommend supplementing with D here.)

One of my Reversing Alopecia course participants shared:  

“My Vitamin D tested at 36 this summer. I doubled my supplementation and retested after three months. It had gone up to 41. That doesn’t seem like much, does it? Is it really that slow to increase? Or is the small change more indicative of an absorption issue?”

1. Magnesium insufficiency
I feel that one of the biggest inhibitors of Vitamin D absorption is magnesium deficiency, which is chronic. Magnesium activates the enzymes that help to metabolize Vitamin D. You can read more about the mag/D relationship here and here.

It’s estimated that 70 percent of the population is deficient in magnesium due to poor soil quality, excessive exposure to nitrogen (largely from fertilizers), phosphorus (largely from soft drinks), copper (largely from water pipes), and iron (largely from excessive red meat and/or supplements). Deficiency can also be a result of taking too much supplemental calcium

Magnesium also promotes a robust immune system and is a proven immune modulator for those with autoimmune conditions.

To read more about magnesium as it relates to thyroid function, go here.

As I quote Dr. Carolyn Dean in my Essential Thyroid Cookbook, “The Recommended Dietary Allowance (RDA) for magnesium is between 350 and 400 milligrams per day, which is just enough to ward off outright deficiency. But for optimal health and for the twenty-two conditions that are triggered by magnesium deficiency, perhaps twice as much magnesium is needed. Because we probably don’t get nearly enough magnesium from our diet, we have to investigate magnesium supplements.” 

There are several types of magnesium and I’m often asked what form to take. According to several in the functional medicine community, the best types of supplemental magnesium are magnesium malate, magnesium glycinate, and magnesium citrate—and many say to avoid magnesium oxide. 

Taking the oil form topically is a good way to get magnesium if taking oral magnesium gives you loose stools. The oil is absorbed directly into the skin and is great for relaxing muscle spasms or soreness.

2. Insufficient dietary fat
Vitamin D is fat-soluble—it needs fat to be absorbed. This is why it’s recommended that we take our D supplement with a meal.

Yes, we need fat and cholesterol. We’re of course talking about a meal with healthful fats, not nasty trans fats.

Additionally, many Vitamin D supplement makers are now adding Vitamin K2 with the D—K2 is also fat-soluble and works synergistically with Vitamin D. Vitamin A in the retinol form (vs. carotenoid) is also fat-soluble and helps with D absorption.

Rich food sources of Vitamin A as retinol include: cod liver oil, shellfish (especially shrimp), wild salmon, sardines, and pastured and/or grassfed butter, ghee, cream, egg yolks, and organ meat (especially liver).

Rich food sources of Vitamin K2 include: fermented soy (natto/tempeh), kefir, and pastured and/or grassfed egg yolks, dark chicken meat, and butter.

3. VDR gene polymorphism
Some carry a gene polymorphism, VDR, that affects the body’s ability to activate Vitamin D.  Thus, having adequate levels of D in blood tests doesn’t mean that they’re able to use all of what’s shown on these labs.

You can read more on the D/VDR relationship here and here

A few of my clients and colleagues carry this SNP (“snip”)/polymorphism. I’m certainly no expert on gene testing and SNPs, but if you’re supplementing with D and not seeing your levels rise, this may be a consideration. 

(Public service announcement: Many are (rightfully) chafed that 23andme (the prior go-to for gene testing) sold exclusive DNA data rights to titan drugmaker, GlaxoSmithKline. Pffft. And ancestry.com has its limitations. You can reach out to me for the best gene testing on the market that comes with a thorough overview of your current health status.)

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