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A Functional Medicine Lactose Intolerance Protocol: Specialty Testing, Elimination Diet, and Supplement Suggestions

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A Functional Medicine Lactose Intolerance Protocol: Specialty Testing, Elimination Diet, and Supplement Suggestions

Lactose intolerance is a condition that is estimated to affect nearly 70% of the world's population. It is characterized by digestive symptoms after consuming foods containing lactose, a sugar naturally found in milk products (1). The prevalence of lactose intolerance varies according to race; as many as 25% of people of southern European descent and 75-90% of Native American, black, and Asian American populations are lactose intolerant (2).

Unlike milk allergy, lactose intolerance cannot cause anaphylaxis but can lead to nutrient deficiencies and associated health complications (1). This is why learning to manage the condition appropriately is important. In this article, we will discuss lactose intolerance and how functional medicine doctors help their patients navigate it through specialty labs, therapeutic dietary modifications, and dietary supplements.


What Is Lactose Intolerance?

Lactose is a sugar found naturally in cow's, goat's, and sheep's milk products unless removed. Lactose is a disaccharide carbohydrate composed of glucose and galactose linked together. Lactose intolerance is the presence of digestive symptoms after ingesting lactose due to lactose malabsorption. Lactose malabsorption, which affects 65% of adults worldwide, is the inability to digest lactose in the first portion of the small intestine, called the duodenum, into its constituents due to low levels of the lactase digestive enzyme. While everyone with lactose intolerance has lactose malabsorption, only those with lactose malabsorption and associated digestive symptoms have lactose intolerance. (1, 5)

Lactose Intolerance Symptoms

As undigested lactose molecules travel through the intestines, bacteria in the colon ferment them, producing gases, and excess water is pulled into the large intestine. This leads to the typical digestive symptoms of lactose intolerance: gas, diarrhea, bloating, and abdominal pain/cramping. Other symptoms may include nausea, vomiting, and stomach rumbling. (3-5)

The timing and severity of symptoms depend on a person's sensitivity, intestinal transit time, and the amount of lactose consumed. While symptoms usually present within 30 minutes to two hours after lactose exposure, they can occur up to two days after eating lactose. (3, 5)

What Causes Lactose Intolerance?

Lactose intolerance is caused by a deficiency in lactase, the digestive enzyme produced by small intestinal cells that breaks down lactose. Lactose intolerance is categorized into three predominant subtypes: congenital, primary, and secondary.

Congenital lactose intolerance, the rarest subtype, is an inherited genetic condition that presents in newborn babies when they first consume milk. (3)

In contrast, primary lactose intolerance is the most common subtype in adults globally and usually presents after childhood. It is associated with aging and the deactivation of lactase genes. Lactase levels decline as these genes are deactivated, and lactose intolerance can develop. Primary lactose intolerance is also referred to as lactase nonpersistence. (3, 4)

Secondary, or acquired, lactase intolerance may develop in small intestinal illness or with certain medications. Small intestinal mucosal damage impairs lactase production, resulting in a deficiency. Causes of secondary lactase deficiency include acute gastrointestinal infections (e.g., rotavirus and giardia), Crohn's disease, celiac disease, small intestinal bacterial overgrowth (SIBO), and diabetes. Medical treatments, such as surgery, chemotherapy, and radiation, can also result in acquired lactose intolerance. Secondary lactose intolerance may not be permanent; lactose tolerance can improve as the small intestine recovers from injury. (3, 5)

Developmental lactose intolerance may occur in premature babies. This differs from congenital lactose intolerance as it is not related to genetics, but instead is secondary to an underdeveloped small intestine. Developmental lactose intolerance usually improves/resolves as the baby ages and the small intestine matures. (5)

Functional Medicine Labs to Test for Lactose Intolerance Diagnosis

Lactose intolerance can be diagnosed clinically based on the presence of lactose-related digestive symptoms that resolve with dietary lactose elimination and return with reintroduction. However, functional medicine providers often utilize labs to confirm the diagnosis, rule out other conditions that can mimic lactose intolerance symptoms, and identify causes of secondary lactose intolerance and factors that increase a patient's lactose sensitivity.

Lactose Malabsorption Breath Test

The lactose hydrogen breath test is the most commonly utilized test to diagnose lactose intolerance in the clinical setting. This test measures hydrogen gas in breath samples collected by the patient at home after they take an oral dose of lactose. A test is considered positive if hydrogen concentrations exceed 20 ppm over baseline within three hours.

SIBO Breath Test

Bacterial overgrowth in the small intestine causes mucosal damage and altered motility, leading to malabsorption of carbohydrates (including lactose). This trio-smart test is another at-home breath test that measures hydrogen, methane, and hydrogen sulfide gas levels exhaled through breath after a patient takes an oral dose of lactulose to assess for the three subtypes of SIBO.

Comprehensive Stool Test

A comprehensive stool test can screen for intestinal infections and signs of underlying inflammatory bowel disorders, such as celiac and Crohn's, by measuring inflammatory markers (calprotectin and lactoferrin).

CICA Assay

The Celiac, IBS, and Crohn's (CICA) Assay is another testing option that can screen for celiac and Crohn's diseases as secondary causes of lactose intolerance. This test cannot definitively rule in either condition, as endoscopy is required as the gold standard for both; however, positive genetic and immune markers can highly suggest their presence.

Micronutrient Test

Avoiding dairy products can lead to calcium and vitamin D deficiencies, which affect the health and function of bones, the nervous system, and the immune system (5). A micronutrient panel helps the provider identify these deficiencies and other nutrient imbalances so that they can recommend appropriate dietary changes and nutritional supplements to support the patient in meeting dietary intake goals.


Functional Medicine Treatment Protocol for Lactose Intolerance

Dietary adjustment is the primary therapy for all patients with lactose intolerance. In secondary lactase deficiency, treatment is directed at the underlying cause. Check out the Rupa Health Magazine for articles discussing treatment strategies and protocols specific to these conditions. Treatment protocols should be personalized based on lab findings and patient preferences. The following treatment protocol can be applied to any case of lactose intolerance, regardless of cause.

Therapeutic Diet and Nutrition Considerations for Lactose Intolerance

A low-lactose diet is the therapeutic dietary intervention recommended for lactose-intolerant people. Most people with lactose intolerance do not require a completely lactose-free diet and can tolerate up to 12-15 grams of lactose daily. Dairy foods are good sources of protein, calcium, phosphorus, potassium, and vitamins A, D, and Bs, and provide health benefits when incorporated in the diet. As such, part of the treatment plan should include experimenting with various dairy products and serving sizes to test the patient's lactose sensitivity and tolerance levels. (3, 6)

A 4-6 week strict dietary elimination of all lactose-containing foods may be recommended by your doctor to observe for resolution of digestive symptoms and make a clinical diagnosis of lactose intolerance. Many plant-based dairy alternatives are commercially available and can enhance elimination compliance. After this, lactose-containing foods are added to the diet every few days to customize the diet per the patient's tolerance.

The following foods contain high amounts of lactose and are generally eliminated or restricted to small quantities (7):

  • Milk, buttermilk, and cream
  • Evaporated and condensed milk
  • Cheese spreads
  • Ice cream
  • Sour cream
  • Whey

The following foods contain smaller amounts of lactose and tend to be better tolerated (7):

  • Hard, aged cheeses (e.g., Swiss, parmesan, cheddar)
  • Cottage, ricotta, and feta cheeses
  • Kefir
  • Reduced-lactose milk
  • Yogurt with live probiotic cultures

Be mindful of foods with hidden sources of lactose, including (3):

  • Bread and baked goods
  • Pancake, biscuit, and cookie mixes
  • Breakfast cereals
  • Instant potatoes, soups, and breakfast drinks
  • Margarine
  • Non-kosher lunch meats
  • Salad dressings
  • Candy

Supplements Protocol for Lactose Intolerance

Functional medicine providers often recommend dietary supplements to supplement diet and lifestyle. The following protocol uses natural products to support lactose digestion, intestinal mucosal healing, and micronutrient status.

Lactase Enzyme

Lactase digestive enzyme can be taken with meals to manage and prevent associated lactose intolerance symptoms. Lactase supports lactose digestion so that elimination from the diet does not need to be as strict, allowing the patient more freedom in dietary choices. Many lactase supplements are on the market, but LACTAID® is a popular and easily accessible over-the-counter brand.

Dose: one serving size (per label instructions) with the first bite of dairy foods

Duration: Ongoing/As needed


Oral Lactobacillus spp. probiotics have been shown to improve lactose hydrogen breath tests and reduce clinical symptoms of diarrhea, abdominal cramping, and vomiting associated with lactose challenges. The most common probiotics used in lactose intolerance protocols include L. acidophilus, L. reuteri, L. rhamnosus, and L. bulgaricus. (8, 9)

Dose: 10 million-10 billion CFU daily

Duration: at least four weeks


L-glutamine is the most abundant amino acid in the blood and the primary fuel source for cells that line the small intestine. L-glutamine is vital in maintaining mucosal integrity by upregulating cell proliferation, repairing damaged cells, and tightening the junctions between small intestinal cells. These properties make L-glutamine a popular first-line gut-healing supplement among functional medicine doctors. (10)

Dose: 5 grams twice daily

Duration: 12 weeks


The recommended dietary allowance (RDA) for calcium varies between 700-1,300 mg depending on sex and age. Patients following a low-lactose diet are at higher risk for not meeting this nutrient requirement, given the elimination/restriction of calcium-rich dairy foods from the diet. A calcium supplement should be recommended to patients not meeting this requirement through diet alone.

Dose: 50-1,000 mg daily

Duration: Ongoing

Vitamin D

Like calcium, patients following a low-lactose diet are also at higher risk for vitamin D deficiency. The vitamin D RDA ranges from 15-20 mcg (600-800 IU) depending on sex and age.

Dose: 1,500-2,000 IU daily

Duration: Ongoing

When to Retest Labs

Repeat labs are not required for patients who respond well to therapy, but they can help monitor treatment progress. This may be especially indicated for those with acquired lactose intolerance to confirm treatment success for underlying causes. Repeat SIBO and stool testing can be performed after eradication therapy has been completed for intestinal infections. Celiac and inflammatory panels can be measured 1-3 months after initiating treatment to monitor intestinal inflammation and gluten exposure. If micronutrient deficiencies are detected at baseline, retest serum levels 4-6 weeks after replacement therapy to ensure adequate dosing.

Patients with acquired lactose intolerance may want to repeat the lactose hydrogen breath test to assess lactose intolerance recovery. This should be performed after the underlying causes of illness have been addressed and the small intestine has been repaired, generally between 3-12 months after the original diagnosis.



Lactose intolerance is a common digestive condition characterized by gastrointestinal symptoms caused by a lactase deficiency. A functional medicine approach to lactose intolerance includes identifying and (if present) treating underlying causes of lactose intolerance and dietary modifications to limit exposure to lactose. Dietary supplements that help manage digestive symptoms and prevent nutritional deficiencies due to dietary restrictions can help achieve treatment goals. This article discussed functional medicine tests and nutritional supplements that can be beneficial to order and recommend to patients with suspected or confirmed lactose intolerance.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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Lab Tests in This Article


1. NIDDK. (2018, February). Definition & Facts for Lactose Intolerance. National Institute of Diabetes and Digestive and Kidney Diseases.

2. Roy, P.K. (2019). Lactose Intolerance: Background, Pathophysiology, Etiology. Medscape.

3. Cloyd, J. (2023, February 28). How To Test for Lactose Intolerance. Rupa Health.

4. NIDDK. (2018, February). Symptoms & Causes of Lactose Intolerance. National Institute of Diabetes and Digestive and Kidney Diseases.

5. Cleveland Clinic. (2023, March 3). Lactose Intolerance. Cleveland Clinic.

6. Dairy. (2020, October 19). Harvard T.H. Chan School of Public Health.

7. Low Lactose Diet. (2022, March 2).

8. Leis, R., de Castro, M.J., de Lamas, C., et al. (2020). Effects of Prebiotic and Probiotic Supplementation on Lactase Deficiency and Lactose Intolerance: A Systematic Review of Controlled Trials. Nutrients, 12(5).

9. Pakdaman, M.N., Udani, J.K., Molina, J.P., et al. (2015). The effects of the DDS-1 strain of lactobacillus on symptomatic relief for lactose intolerance - a randomized, double-blind, placebo-controlled, crossover clinical trial. Nutrition Journal, 15(1).

10. Rao, R., & Samak, G. (2012). Role of Glutamine in Protection of Intestinal Epithelial Tight Junctions. Journal of Epithelial Biology and Pharmacology, 5(1), 47–54.

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