Protocols
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June 15, 2023

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

Written By
Dr. Jaime Cloyd ND
Medically Reviewed by
Updated On
January 13, 2025

An estimated 68% of the global population experiences some degree of lactose intolerance, making it one of the most common digestive concerns worldwide. For many, the simple pleasure of consuming dairy can lead to discomfort. In the long term, lactose intolerance may affect health by contributing to nutrient deficiencies. This is why learning to manage the condition appropriately is important.

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What Is Lactose Intolerance?

Lactose is a sugar (called a disaccharide, composed of one glucose and one galactose molecule linked together) found naturally in cow's, goat's, and sheep's milk products unless removed. 

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. (9, 14)

Lactose Intolerance Signs & Symptoms

When lactase levels are insufficient, undigested lactose travels into the colon. Here, lactose draws water into the colon and undergoes fermentation by the resident bacteria, producing excess gases. The increase of water and gas in the colon leads to the hallmark symptoms of lactose intolerance, which include:

  • Gas
  • Diarrhea
  • Bloating
  • Abdominal pain/cramping (2, 8, 14)

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. (2, 14)

Root Causes of 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 four predominant subtypes: congenital, primary, secondary, and developmental.

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

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. (2, 8)

Secondary, or acquired, lactase intolerance may develop in small intestinal illness or with certain medications. Small intestinal mucosal damage impairs lactase production, resulting in an enzymatic deficiency. Causes of secondary lactase deficiency include acute gastrointestinal infections (e.g., rotavirus and giardia), Crohn's disease, celiac disease, and small intestinal bacterial overgrowth (SIBO). 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. (2, 14)

Developmental lactose intolerance may occur in premature babies. This differs from congenital lactose intolerance as it is not related to genetics but is secondary to an underdeveloped small intestine. Developmental lactose intolerance usually improves/resolves as the baby ages and the small intestine matures. (14)

How to Diagnose Lactose Intolerance

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, the following steps can be taken to confirm the diagnosis, rule out other conditions that mimic lactose intolerance symptoms, and identify the causes of secondary lactose intolerance.

Step 1: Lactose Intolerance Tests

The lactose hydrogen breath test is the most commonly utilized test to diagnose lactose intolerance in the clinical setting because it is positive in 90% of patients with lactose malabsorption. 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. Recent use of oral antibiotics, recent high colonic enema, and smoking may lead to inaccurate results. (22

The following lactose hydrogen breath tests are available to order through Rupa Health:

Alternatively, the lactose tolerance test involves administering an oral dose of 1-1.5 grams of lactose per kilogram of body weight and measuring serial blood glucose levels over two hours. The test is positive if intestinal symptoms occur and blood glucose increases less than 20 mg/dL (1.1 mmol/L) above the fasting level. This test is less commonly utilized because it has a higher rate of false-positive and false-negative results than the lactose hydrogen breath test. (22)

Step 2: Tests to Investigate the Root Cause of Lactose Intolerance

Patients with secondary lactose intolerance require additional evaluation to identify the primary underlying problem. 

Tests that can be considered include those to rule out SIBO, celiac disease, Crohn's disease, and acute gastrointestinal infection. The following labs can help do so:

Step 3: Tests to Customize Lactose Intolerance Management Plans

Exclusion of dairy products from the diet can lead to nutrient deficiencies, as dairy is a major source of calcium, phosphorus, choline, riboflavin, vitamin B12, and vitamin A in the United States (7).

The following micronutrient tests help doctors identify nutrient insufficiencies and better recommend appropriate nutritional strategies for meeting nutritional intake goals: 

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Management Plan for Lactose Intolerance

Dietary adjustment is the primary approach for all patients with lactose intolerance. Management plans should be personalized based on lab findings and patient preferences. The following management plan can be applied to any case of lactose intolerance, regardless of cause.

Step 1: Low-Lactose Diet

Here's Why This Is Important:

A low-lactose diet is the dietary approach recommended for lactose-intolerant people. 

How Do You Do This?

Most people with lactose intolerance do not require a completely lactose-free diet and can tolerate up to 12-15 grams of lactose (equivalent to 8-12 oz of milk) daily. Dairy foods are good sources of protein, calcium, phosphorus, potassium, and vitamins A, D, and Bs, and they provide health benefits when incorporated into the diet. As such, part of the management plan should include experimenting with various dairy products and serving sizes to test the patient's lactose sensitivity and tolerance levels. (22)

Your doctor may recommend a 4-6 week strict dietary elimination of all lactose-containing foods to observe the 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 reintroduced every few days to customize the diet according to the patient's tolerance.

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

  • Milk, buttermilk, and cream
  • Evaporated and condensed milk
  • Cheese spreads
  • Ice cream
  • Sour cream
  • Whey (15)

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

  • Hard, aged cheeses (e.g., Swiss, parmesan, cheddar)
  • Cottage, ricotta, and feta cheeses
  • Kefir
  • Reduced-lactose milk
  • Yogurt with live probiotic cultures (15)

Be mindful of foods with hidden sources of lactose, including (2):

  • 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

Step 2: Nutritional Support

Here's Why This Is Important:

Nutritional support, including digestive enzymes, dietary supplements, and probiotics, helps individuals with lactose intolerance maintain optimal health and manage their digestive symptoms.

How Do You Do This?

Patients following a low-lactose diet may need to consider calcium and vitamin D supplements to help meet their nutritional needs. The RDAs for calcium and vitamin D vary depending on sex and age:

Lactase enzyme supplements, such as LACTAID®, can be taken with lactose-containing meals to help manage clinical symptoms. Lactase enzymes support lactose digestion, so elimination from the diet does not need to be as strict, allowing the patient more freedom in dietary choices.

Oral Lactobacillus spp. probiotics, administered in doses ranging from 10 million to 10 billion CFU daily, have been shown to support digestive health and may help manage symptoms associated with lactose challenges. The most common probiotics used in lactose intolerance protocols include L. acidophilus, L. reuteri, L. rhamnosus, and L. bulgaricus. (16, 19)

Step 3: Address the Underlying Cause

In secondary lactase deficiency, management is directed at the underlying cause. Strategies may include:

  • Antibiotics or herbal antimicrobials to help manage SIBO or other gastrointestinal infections
  • Gluten-free diet for managing celiac disease
  • Anti-inflammatory and immunomodulating approaches to support Crohn's disease management

You can check out the Rupa Health Magazine for articles discussing management strategies and protocols specific to these conditions.

The Considerations of Lactose Intolerance

Eating lactose will not cause any permanent damage to the gastrointestinal tract. However, if not managed properly, one of the primary concerns of lactose intolerance is nutritional deficiency – particularly of calcium and vitamin D. These nutrients are important for maintaining bone health, and their deficiency can lead to osteoporosis and increased fracture risk. (18)

Misdiagnosis or self-diagnosis of lactose intolerance without professional guidance can lead to overlooking conditions like celiac disease or inflammatory bowel disease, which can lead to permanent gastrointestinal damage and severe complications when not addressed appropriately.

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Key Takeaways:

  • Lactose intolerance is a common digestive condition characterized by gastrointestinal symptoms caused by a lactase deficiency. 
  • A holistic approach to managing lactose intolerance includes identifying and (if present) addressing underlying causes of lactose intolerance while implementing dietary modifications to limit lactose exposure. Precautions should also be taken to manage digestive symptoms and support nutritional needs due to dietary restrictions.
The information in this article is designed for educational purposes only and is not intended to be a substitute for informed medical advice or care. This information should not be used to diagnose or treat any health problems or illnesses without consulting a doctor. Consult with a health care practitioner before relying on any information in this article or on this website.

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Lab Tests in This Article

  1. Baijal, R., & Tandon, R. K. (2020). Effect of lactase on symptoms and hydrogen breath levels in lactose intolerance: A crossover placebo‐controlled study. JGH Open, 5(1), 143–148. https://doi.org/10.1002/jgh3.12463
  2. Cloyd, J. (2023, February 28). How To Test for Lactose Intolerance. Rupa Health. https://www.rupahealth.com/post/how-to-test-for-lactose-intolerance
  3. Cloyd, J. (2023, March 14). SIBO Testing 101: A Complete Guide to The Top 3 SIBO Tests. Rupa Health. https://www.rupahealth.com/post/sibo-testing-101-a-complete-guide-to-the-top-3-sibo-tests
  4. Cloyd, J. (2023, November 1). How To Interpret Your Celiac Blood Test Results. Rupa Health. https://www.rupahealth.com/post/how-to-interpret-your-celiac-blood-test-results
  5. Dairy. (2020, October 19). The Nutrition Source; Harvard T.H. Chan School of Public Health. https://www.hsph.harvard.edu/nutritionsource/dairy/
  6. Dominici, S., Marescotti, F., Sanmartin, C., et al. (2022). Lactose: Characteristics, Food and Drug-Related Applications, and Its Possible Substitutions in Meeting the Needs of People with Lactose Intolerance. Foods, 11(10), 1486. https://doi.org/10.3390/foods11101486
  7. Facioni, M. S., Raspini, B., Pivari, F., et al. (2020). Nutritional Management of Lactose intolerance: the Importance of Diet and Food Labelling. Journal of Translational Medicine, 18(1). https://doi.org/10.1186/s12967-020-02429-2
  8. Fisher, R. (2019, February 22). Symptoms & Causes of Lactose Intolerance. National Institute of Diabetes and Digestive and Kidney Diseases. https://www.niddk.nih.gov/health-information/digestive-diseases/lactose-intolerance/symptoms-causes
  9. Fisher, R. (2019, April 11). Definition & Facts for Lactose Intolerance. National Institute of Diabetes and Digestive and Kidney Diseases. https://www.niddk.nih.gov/health-information/digestive-diseases/lactose-intolerance/definition-facts
  10. Greenan, S. (2021, November 2). Constant Burping Is A Sign Of This Harmful Bacterial Overgrowth. Rupa Health. https://www.rupahealth.com/post/a-functional-medicine-approach-to-sibo
  11. Henry, E. (2021, July 12). Stool Testing 101: A Complete Guide to the Top 3 Gut Health Tests. Www.rupahealth.com. https://www.rupahealth.com/post/stool-testing-101-a-complete-guide-to-the-top-4-microbiome-tests
  12. Khakham, C. (2023, August 11). Top Labs To Run Bi-Annually On Your Patients Who Suffer From Lactose Intolerance. Rupa Health. https://www.rupahealth.com/post/top-labs-to-run-bi-annually-on-your-patients-who-suffer-from-lactose-intolerance
  13. LACTAID® Dietary Supplements. LACTAID®. https://www.lactaid.com/products/lactaid-dietary-supplements
  14. Lactose Intolerance. (2023, March 3). Cleveland Clinic. https://my.clevelandclinic.org/health/diseases/7317-lactose-intolerance
  15. Lactose-Controlled Diet. Drugs.com. https://www.drugs.com/cg/low-lactose-diet.html
  16. 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). https://doi.org/10.3390/nu12051487
  17. Maholy, N. (2023, February 24). Integrative Medicine Treatment Protocol for Giardia. Rupa Health. https://www.rupahealth.com/post/integrative-medicine-treatment-protocol-for-giardia
  18. Malik, T. F., & Panuganti, K. K. (2019). Lactose Intolerance. PubMed; StatPearls Publishing. https://www.ncbi.nlm.nih.gov/books/NBK532285/
  19. 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). https://doi.org/10.1186/s12937-016-0172-y
  20. Roy, P. K. (2021). Lactose Intolerance: Background, Pathophysiology, Etiology. Medscape. https://emedicine.medscape.com/article/187249-overview#a6
  21. Shaukat, A. (2010). Systematic Review: Effective Management Strategies for Lactose Intolerance. Annals of Internal Medicine, 152(12), 797. https://doi.org/10.7326/0003-4819-152-12-201006150-00241
  22. Swagerty Jr. , D. L., Walling, A. D., & Klein, R. M. (2002). Lactose Intolerance. American Family Physician, 65(9), 1845–1851. https://www.aafp.org/pubs/afp/issues/2002/0501/p1845.html#diagnosis
  23. Sweetnich, J. (2023, March 28). Calcium 101: Testing, top foods, & supplements. Rupa Health. https://www.rupahealth.com/post/calcium-101-testing-top-foods-supplements
  24. Sweetnich, J. (2023, May 4). Vitamin D 101. Rupa Health. https://www.rupahealth.com/post/vitamin-d-101-testing-rdas-and-supplementing
  25. Weinberg, J. L. (2022, February 28). An Integrative Medicine Approach to Celiac Disease. Rupa Health. https://www.rupahealth.com/post/a-functional-medicine-approach-to-celiac-disease
  26. Weinberg, J. L. (2022, April 14). Crohn's Disease Symptoms, Causes, And Treatment Options. Rupa Health. https://www.rupahealth.com/post/a-functional-medicine-approach-to-crohns-disease
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