What Illness Causes Low Vitamin D? Understanding Deficiency

January 8, 2026 •

3 min read

According to the CDC, vitamin D deficiency is widespread, and in many cases, it is caused by an underlying medical condition. These illnesses interfere with your body's ability to produce, absorb, or activate vitamin D, leading to significantly low levels. Understanding what illness causes low vitamin D is crucial for proper diagnosis and treatment.

Quick Summary

This article details the key medical conditions that lead to vitamin D deficiency, covering malabsorption syndromes, chronic kidney and liver diseases, and other contributing factors. It explains the biological mechanisms and associated risks for a comprehensive overview.

Key Points

Malabsorption Syndromes: Conditions like Celiac disease, Crohn's disease, and Cystic Fibrosis hinder the absorption of fat-soluble vitamins, including vitamin D, from the gut.
Chronic Organ Diseases: Chronic liver and kidney diseases impair the body's ability to convert vitamin D into its active, usable form.
Genetic Disorders: Rare hereditary conditions like Vitamin D-dependent rickets prevent the activation of or cellular response to vitamin D, despite normal intake.
Obesity: Excess body fat can sequester vitamin D, making it less bioavailable in the bloodstream, and may necessitate higher supplement doses.
Systemic Inflammation: Chronic inflammatory states common in many diseases can contribute to and be worsened by low vitamin D levels, creating a negative feedback loop.
Certain Medications: Some drugs, including anticonvulsants, accelerate the breakdown of vitamin D in the liver, leading to lower levels.
Autoimmune Conditions: Diseases like lupus are linked with vitamin D deficiency, although the relationship is complex and often bidirectional.

Vitamin D is an essential nutrient with a crucial role in bone health, immune function, and overall well-being. While many people associate low vitamin D with insufficient sun exposure, a number of underlying medical conditions can significantly contribute to or directly cause a deficiency. These illnesses impact the body's complex process of converting sunlight and dietary intake into the usable form of the vitamin. Understanding the specific health issues that can lead to low vitamin D is essential for effective diagnosis and management.

Malabsorption Syndromes and Fat Digestion Issues

Conditions that impair the digestion or absorption of dietary fat can lead to vitamin D deficiency because it is a fat-soluble vitamin.

Celiac Disease: This autoimmune disorder damages the small intestine, leading to malabsorption of nutrients, including fat-soluble vitamins.
Crohn's Disease and Other Inflammatory Bowel Diseases (IBD): Chronic inflammation in the digestive tract can reduce vitamin D absorption.
Cystic Fibrosis (CF): A genetic disorder where thick mucus blocks pancreatic enzymes, causing severe fat malabsorption and common vitamin D deficiency.
Chronic Pancreatitis: Inflammation of the pancreas can impair fat digestion and vitamin D absorption.
Bariatric Surgery: Certain weight-loss procedures can cause malabsorption and increase the risk of deficiency.

Organ-Specific Conditions That Disrupt Metabolism

Some diseases prevent the body from metabolizing vitamin D into its active form, requiring proper liver and kidney function.

Chronic Liver Disease

The liver performs a crucial step in converting vitamin D to a usable form. Chronic liver disease impairs this process, leading to vitamin D insufficiency in many affected individuals due to impaired hydroxylation and reduced binding protein production.

Chronic Kidney Disease (CKD)

The kidneys complete the activation of vitamin D into calcitriol. In CKD, especially in later stages, this function is lost, resulting in active vitamin D deficiency which affects bone, cardiovascular, and immune health.

Genetic and Hereditary Disorders

Rare genetic disorders can cause deficiency by affecting vitamin D metabolism or cellular response.

Hereditary Rickets: Vitamin D-dependent rickets (VDDR) involves gene mutations that impair vitamin D activation in the liver or kidneys, or cause cellular resistance to the vitamin.
Congenital Hypophosphatemic Rickets: This genetic condition causes excessive phosphate loss by the kidneys, affecting bone mineralization.

Other Contributing Medical Conditions

Obesity: Higher BMI is linked to lower serum vitamin D levels, possibly because the vitamin is stored in fat tissue. Higher supplement doses may be needed in obese individuals.
Medications: Certain drugs, like anticonvulsants, can speed up vitamin D breakdown in the liver.
Autoimmune Diseases: Many autoimmune disorders, such as lupus, are associated with low vitamin D, potentially due to complex interactions between vitamin D and the immune system.

The Role of Systemic Inflammation

Chronic inflammation, present in many illnesses, may contribute to reduced vitamin D levels. This creates a cycle where inflammation lowers vitamin D, and deficiency may worsen inflammation.

Comparison of Major Illnesses and Their Effect on Vitamin D


Illness	Primary Mechanism for Low Vitamin D	How it Affects the Body	Impact on Vitamin D Levels
Celiac Disease	Fat malabsorption due to intestinal damage.	Autoimmune response to gluten damages small intestine lining.	Prevents absorption of dietary vitamin D.
Chronic Kidney Disease	Impaired conversion to active form.	Diseased kidneys lack the enzymes for the final activation step.	Directly causes deficiency of the active form of vitamin D (calcitriol).
Chronic Liver Disease	Impaired conversion to active form.	Diseased liver lacks the enzymes for the initial conversion step.	Prevents the conversion of dietary and sun-derived vitamin D to its storage form.
Cystic Fibrosis	Fat malabsorption due to pancreatic dysfunction.	Thickened mucus blocks pancreatic enzymes from reaching the gut.	Leads to very high rates of severe vitamin D deficiency.
Obesity	Sequestration in adipose tissue.	Vitamin D is stored in excess fat, reducing circulating levels.	Associated with lower circulating vitamin D, may require higher doses of supplementation.

Conclusion

Beyond insufficient sun exposure, numerous illnesses cause low vitamin D by disrupting absorption or metabolism. Malabsorption syndromes, liver and kidney diseases, genetic conditions, obesity, and chronic inflammation all play a role. Identifying and treating the underlying condition is crucial for managing persistent deficiency and preventing complications. Consulting a healthcare provider is essential for diagnosis and a personalized treatment plan.

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Frequently Asked Questions

Yes, Crohn's disease is an inflammatory bowel disease that can cause fat malabsorption, particularly if it affects the small intestine. This malabsorption significantly reduces your body's ability to absorb the fat-soluble vitamin D from food and supplements.

The kidneys are responsible for the final conversion of vitamin D into its active hormonal form, calcitriol. When kidney function is impaired, as in chronic kidney disease, this conversion process is disrupted, leading to low levels of active vitamin D.

Obesity is a strong risk factor for vitamin D deficiency, primarily because vitamin D is sequestered in the larger volume of fat tissue. This reduces the amount of circulating vitamin D, though the exact relationship is still being studied.

Yes, chronic liver disease can interfere with the first crucial step of vitamin D metabolism. The liver's reduced ability to convert vitamin D into its storage form (25-hydroxyvitamin D) directly contributes to a deficiency.

Certain rare genetic disorders, such as Vitamin D-dependent rickets, affect the genes responsible for vitamin D metabolism or the function of the vitamin D receptor. This prevents the body from activating or responding to the vitamin properly, regardless of intake.

Systemic inflammation, common in chronic illnesses like IBD, can negatively affect vitamin D levels. Conversely, vitamin D has anti-inflammatory properties, so a deficiency can worsen inflammation, creating a bidirectional relationship.

Patients with Celiac disease often have significant fat malabsorption leading to vitamin D deficiency, especially at diagnosis. While a gluten-free diet can improve absorption over time, many still require ongoing vitamin D supplementation, often at higher doses, to maintain optimal levels.