Vitamin D deficiency is commonly associated with autoimmune conditions such as Hashimoto’s hypothyroidism and type 1 diabetes, as well as muscle pain, neurodegenerative disorders, osteoporosis, impaired wound healing, depression, constant fatigue, and more.

Understanding the role of vitamin D and how to maintain proper testing, supplementation, and cofactors will go a long way in fostering balanced immune system function.

Factors contributing to vitamin D deficiency

Modern diets typically lack vitamin D-rich foods — liver, organ meats, seafood, butter, and egg yolks — which has led to gross deficiency in the United States. Even eating plenty of these foods, it’s hard to get enough vitamin D.

Lack of sunshine: The primary source for vitamin D for most people is solar ultraviolet-B (UVB). However, despite exposure to adequate sunlight, the prevalence of vitamin D deficiency is high. I even see a vitamin D deficiency in almost all of my patients here in sunny San Diego.

People using UVB tanning beds or sunbathing weekly in southern locations may not need supplemental vitamin D, however the higher north you live or the darker your skin, the greater your vitamin D need.

Gastrointestinal inflammatory disorders reduce absorption of vitamin D.

Cortisol elevations or use of cortisone can deplete vitamin D levels.

Mobility: People who are house-bound or rarely get outside (such as in nursing homes) are not able to use sun exposure to produce vitamin D. Windows prevent vitamin D production from sunlight.

As we age we become less efficient in using sunlight to make vitamin D.

Adrenal stress and obesity also contribute to vitamin D deficiency.

Vitamin D deficiency common in Hashimoto’s patients

Research shows vitamin D plays a critical role in the development of immune system balance, general tolerance to environmental chemicals, and immune barrier integrity.

Vitamin D appears to influence the activity of the immune system’s regulatory T-cells and the balance of TH-1/ TH-2 cells, which have a profound impact on the systemic inflammation underlying all autoimmune conditions.

When it comes to autoimmunity, the problem of a vitamin D deficiency is made worse by genetics — studies show more than 90 percent of people with autoimmune disease have a genetic defect affecting their ability to process vitamin D.

Many autoimmune patients need higher amounts of vitamin D to maintain health even if a blood test shows sufficient vitamin D. This is because the defect is in their cells’ vitamin D receptors, so that even if it’s prevalent in the bloodstream, not enough of the nutrient can gain entry into the cells.

Other consequences of vitamin D deficiency

Chronic muscle pain

Vitamin D deficiencies may cause chronic diffuse nonspecific musculoskeletal pain that is associated with both muscle and bone pain.

Ethnicities with darker skin appear to be at more risk for vitamin D insufficiencies in general, but specifically as it relates to chronic nonspecific musculoskeletal pain. One study found that 16 percent of Asians, 40 percent of Hispanics and Native Americans, and 50 percent of African Americans with chronic nonspecific musculoskeletal pain demonstrate severe vitamin D deficiencies.


Individuals who are deficient in vitamin D are at higher risk of insulin resistance and metabolic syndrome. Research has demonstrated preventative roles for vitamin D for type I diabetes mellitus.

Neurodegenerative disorders

Vitamin D has demonstrated many influential roles in neurodegenerative disease such as multiple sclerosis. Vitamin D supplementation has exhibited diminished relapse rates.

Bone metabolism and osteoporosis

Vitamin D is important for regulation of both calcium and phosphorus absorption and metabolism. There is a direct relationship between serum 25 (OH) D levels and bone in health in both males and females for all age groups.

Vitamin D in pregnancy, infancy, and childhood

Associations with vitamin D insufficiency during pregnancy and low birth weight have been published. Research has also shown that there are increased maternal bone density losses during pregnancy when vitamin D deficiency is present. Adequate maternal vitamin D status is important for proper tooth and metabolism and reduces the risk of development of type I diabetes. Inadequate vitamin D intake in infancy can lead to unhealthy bone metabolism and increased risk of fractures.

Vitamin D testing

Make sure to test your vitamin D levels with a serum 25-hydroxy vitamin D test. On a lab test, I like to see high-normal vitamin D levels for patients with thyroid disorders. Your level should be around 50 ng/mL. Levels above 100 ng/mL may indicate a vitamin D overload.

Retest vitamin D levels periodically

Gut health can affect absorption of vitamin D. If you are working on healing your leaky gut, your absorption might improve. Retesting to gauge your vitamin D levels will help you maintain proper supplementation levels without vitamin D overload.

Vitamin D dosing

Many experts on vitamin D research have considered current dosage guidelines for vitamin D to be obsolete; they are based solely on the maintenance of bone health and do not account for the influence of vitamin D for autoimmunity.

Vitamin D has been shown to help dampen autoimmunity. However, with autoimmunity you cannot just take RDA amounts of vitamin D and expect a response.

In the absence of exposure to sunlight, a minimum of 1,000 IU of vitamin D3 is required to maintain a healthy concentration of 25-hydroxy vitamin D3 in the blood.

However, typical doses of vitamin D for autoimmunity can be anywhere from 5,000 to 10,000 IU per day. Some may take higher doses, but if you do, you should test your vitamin D levels periodically.

Emulsified vitamin D

Emulsification of vitamin D is important so that someone with poor digestion can absorb the nutrient. It also helps prevent toxicity at higher doses.

Emulsified vitamin D3 (cholecalciferol) is a powerful immune modulator that has better bioavailability than ergocalciferol (D2), which has been shown to be ineffective at raising serum vitamin D levels.

Emulsified vitamin D3 best supports the T-regulatory cells when prescribed in therapeutic doses by a licensed healthcare practitioner qualified to work with vitamin D therapy.

Cod liver oil, although high in vitamin D and possessing necessary cofactors for its absorption, does not provide enough of the vitamin to modulate an autoimmune disease. Taken in large amounts, cod liver oil also delivers too much EPA and DHA, which has blood-thinning properties.

Vitamin D cofactors

The conversion of vitamin D3 (cholecalciferol) into active vitamin 25(OH) D includes many cofactors such as magnesium, biotin, pantethine, calcium, and boron. Along with vitamin D, these cofactors support immune system separately or through strengthening the physiological effects of vitamin D. Calcium and magnesium are of importance in intracellular metabolic functions regulated mainly via hormonal signals.

The Vitamin D Council offers more information and vitamin D test kits at www.vitamindcouncil.org.