Why are my intestines not absorbing vitamin D?: A Deep Dive into Malabsorption Causes

October 10, 2025 •

4 min read

According to the National Institutes of Health, billions of people worldwide are estimated to have vitamin D deficiency. One often-overlooked culprit behind persistently low levels is intestinal malabsorption, which provides the answer to the question: why are my intestines not absorbing vitamin D? effectively.

Quick Summary

Several underlying conditions, such as celiac disease, IBD, and pancreatic insufficiency, can cause poor vitamin D absorption. Surgical procedures, certain medications, and obesity are also factors.

Key Points

Underlying Medical Conditions: Diseases like Celiac, Crohn's, and cystic fibrosis can directly damage the intestinal lining or block digestive enzymes, preventing vitamin D absorption.
Fat is Essential: As a fat-soluble vitamin, vitamin D requires the presence of dietary fat and bile acids for proper emulsification and absorption in the intestines.
Surgical Impacts: Weight-loss surgeries, particularly gastric bypass, can significantly reduce the intestinal surface area and alter digestive processes, leading to malabsorption.
Medication Interference: Certain drugs, including corticosteroids and cholesterol-lowering agents, can interfere with the body's metabolism and absorption of vitamin D.
Testing is Key: Diagnosing malabsorption involves a combination of blood tests for nutrient levels, stool tests for fat content, and sometimes more invasive procedures like a small intestine biopsy.
Strategic Supplementation: If malabsorption is confirmed, dietary strategies like pairing supplements with fat or using alternative delivery methods, such as buccal sprays, may be more effective.

Understanding the Complex Path of Vitamin D Absorption

Vitamin D is a crucial fat-soluble nutrient, playing a vital role in maintaining bone health, immune function, and regulating calcium levels. While sun exposure allows the skin to produce vitamin D, dietary intake and supplementation are also significant sources. When vitamin D is consumed, it is absorbed through a sophisticated process that relies heavily on dietary fat and the proper functioning of the small intestine, liver, and pancreas.

The absorption process begins when dietary fats stimulate the release of bile acids from the gallbladder and digestive enzymes from the pancreas into the small intestine. These substances work together to emulsify fat-soluble vitamins, including vitamin D, into micelles, making them transportable across the intestinal wall. Once absorbed by the intestinal lining cells, vitamin D is packaged into lipoproteins called chylomicrons and transported into the bloodstream via the lymphatic system. Any condition that disrupts this delicate chain of events can lead to malabsorption, causing vitamin D deficiency despite adequate oral intake.

Medical Conditions Affecting Intestinal Malabsorption

Damage to the intestinal lining, impaired bile or enzyme production, and other chronic conditions are primary reasons for vitamin D malabsorption. These issues prevent the intestines from properly processing and absorbing nutrients.

Digestive System Disorders

Celiac Disease: This autoimmune disorder causes an inflammatory response to gluten, damaging the absorptive surface of the small intestine. The resulting villous atrophy significantly reduces the intestine's ability to absorb nutrients, including vitamin D.
Inflammatory Bowel Disease (IBD): Conditions like Crohn's disease and ulcerative colitis cause chronic inflammation throughout the digestive tract, which can interfere with the absorption of fat and other nutrients.
Chronic Pancreatic Insufficiency (PI): PI is characterized by the pancreas's inability to produce enough digestive enzymes, which are critical for breaking down dietary fats. This leads to fat malabsorption (steatorrhea) and, consequently, poor vitamin D uptake.
Cystic Fibrosis: In this genetic disease, thick mucus can block the pancreatic ducts, preventing the release of digestive enzymes and causing severe fat malabsorption.

Liver and Kidney Dysfunction

Chronic Liver Disease: Since bile production is a liver function, chronic liver disease can lead to insufficient bile, which is necessary for fat emulsification and vitamin D absorption. The liver is also the site of the first step in converting vitamin D into its active form.
Kidney Disease: While not directly an intestinal issue, kidney disease impairs the final activation step of vitamin D, preventing the body from utilizing it effectively.

Other Causes of Poor Vitamin D Absorption

Malabsorption isn't limited to digestive diseases. Other physiological changes and external factors can also play a role. Bariatric surgery procedures, certain medications like corticosteroids, and obesity have been associated with vitamin D malabsorption. Genetic variations may also play a role.

Diagnostic Approach to Identifying the Cause

If malabsorption is suspected, a healthcare provider may conduct tests such as serum 25(OH)D level to measure vitamin D status. A fecal fat test can measure fat content in stool, while a D-Xylose absorption test checks small intestine function. An endoscopy with biopsy may be used to examine the intestinal lining for damage.

Management and Treatment Strategies

Effective management requires addressing the root cause, as simply increasing oral supplements may not be enough. Treatment for conditions like Celiac disease, IBD, or pancreatic insufficiency can involve dietary changes, medication, or enzyme replacement. Pairing oral vitamin D with fat can enhance absorption, and in severe cases, alternative methods like sprays or injections may be necessary.

Comparison: Normal Absorption vs. Malabsorption


Feature	Normal Vitamin D Absorption	Vitamin D Malabsorption
Mechanism	Efficient emulsification by bile and packaging into chylomicrons for lymphatic transport.	Impaired emulsification or uptake due to disease, leading to insufficient chylomicron formation.
Intestinal Lining	Healthy, intact intestinal villi provide a large surface area for absorption.	Damaged villi (Celiac disease) or inflamed lining (IBD) reduces absorptive area.
Associated Nutrients	Vitamin D is easily absorbed alongside dietary fat.	Reduced absorption of other fat-soluble vitamins (A, E, K) is also common.
Common Symptoms	Healthy nutrient status, strong bones, normal calcium levels.	Fatigue, bone and muscle pain, weakness, low blood calcium, and increased fracture risk.
Primary Cause	No underlying digestive issues.	Celiac disease, Crohn's, cystic fibrosis, pancreatic insufficiency, bariatric surgery.

Conclusion

While factors like limited sun exposure are widely known causes of low vitamin D, a surprising number of individuals have impaired absorption due to underlying gastrointestinal issues. Conditions such as celiac disease, inflammatory bowel disease, and liver or pancreatic disorders can directly inhibit the intestines' ability to process this vital nutrient. Surgical interventions like gastric bypass and certain medications also play a significant role. Identifying the root cause through proper diagnosis is the first and most critical step toward effective management. By treating the underlying condition and employing specific dietary strategies, it is possible to restore adequate vitamin D levels and mitigate the associated health risks. Working with a healthcare provider and a registered dietitian is key to creating a personalized plan for restoring optimal nutrient absorption. {Link: NIH https://ods.od.nih.gov/factsheets/VitaminD-HealthProfessional/}

Frequently Asked Questions

The primary signs are often symptoms of vitamin D deficiency, including fatigue, bone and muscle pain, unexplained weight loss, and in severe cases, osteomalacia in adults or rickets in children.

Chronic liver disease, such as cirrhosis, can impair the liver's ability to produce bile, which is essential for emulsifying and absorbing fat-soluble vitamins like vitamin D. It can also reduce the enzymes needed to convert vitamin D into its active form.

Not always. While supplements are often prescribed, if the underlying malabsorption issue is not addressed, the body may still not absorb the supplemental vitamin D effectively. Higher doses or alternative delivery methods might be needed, as advised by a doctor.

Yes, because vitamin D is fat-soluble, consuming it with a meal containing fat can significantly increase its absorption. This is why many supplements are oil-based.

Both vitamin D2 (ergocalciferol) and D3 (cholecalciferol) are absorbed in the small intestine. While D3 is generally considered more effective at raising serum vitamin D levels, the absorption mechanism in the intestine is similar for both forms and dependent on fat.

Yes. Research suggests that vitamin D helps maintain the integrity of the intestinal barrier. An imbalanced gut microbiome can lead to inflammation and damage the barrier, potentially impairing vitamin D absorption.

In addition to standard blood tests for vitamin D levels, a doctor may order a fecal fat test to check for fat malabsorption, a D-xylose absorption test to check intestinal function, or a small intestine biopsy.