This article was written for a magazine for general practitioners in 2023.

Written by Registered Dietitian Nishti

There is a lot of confusion about lactose intolerance and cow’s milk allergy and the diagnostic terms are often used interchangeably, resulting in inaccurate diagnosis and treatment modalities (1). Lactose is often excluded if an infant struggles to digest their milk, however, before excluding lactose from the diet, it is important to understand the difference between lactose intolerance and cow’s milk allergy as these are different medical conditions that both require distinct treatments.

This article aims to provide an overview of the difference between the two. 

What is Lactose?

Lactose is a disaccharide and the main sugar found in mammalian milk and milk products. Both breastmilk and infant formula, whose composition is based on breastmilk, provide up to 50% of the total energy of the milk (2). Lactose is digested by the enzyme lactase. Digestion and absorption of lactose takes place in the small intestine with lactase having its highest expression in the mid-jejunum (3). 

What is Lactose Intolerance?

  • There are four clinical types of lactose intolerance: developmental lactase deficiency, congenital lactase deficiency, lactase non-persistence, and secondary lactose intolerance (See table below).
  • The term ‘Lactase deficiency’ describes the state of reduced lactase expression, compared to term infants and ‘Lactose intolerance’ is clinically defined as lactose malabsorption with associated gastrointestinal symptoms (1).

Secondary Lactose Intolerance

In young children, the most common causes of secondary lactose intolerance include gastroenteritis and cow’s milk allergy (14). Lactase enzyme is very sensitive to any type of bowel injury or distress which can cause lower levels of lactase. Lower levels of lactase result in undigested lactose passing through the gut and cause symptoms associated with lactose intolerance. Secondary lactose intolerance is acute and should resolve no later than 6 weeks once the epithetical cells have recovered. If symptoms revert and if additional symptoms are present, consider non-IgE CMA. 

Cow’s Milk Allergy

Milk allergy can be either immunoglobulin E (IgE) or non-IgE mediated. IgE-mediated reactions typically occur immediately after ingestion whereas non-IgE mediated are delayed and take up to 72 hours to develop. Both IgE and non-IgE involve the immune system whereas lactose intolerance does not involve the immune system. The symptoms of non-IgE mediated disease are wrongly labeled as symptoms of intolerance, using the term ‘lactose intolerance’ (6). Unless there is enteropathy, with small bowel damage causing secondary lactose intolerance, most infants with cow’s milk allergy can tolerate lactose (7). 

Non-IgE Cow’s Milk Allergy – diagnosis and treatment

There are no validated tests for the diagnosis of non-IgE CMA, apart from avoidance of cow’s milk followed by a reintroduction challenge to confirm the diagnosis (8). 

All dairy products must be removed from the diet of a breastfeeding mother and calcium supplements given. If the baby is formula-fed, a hypoallergenic formula must be trailed. The choice of the formula is based on the severity of symptoms but usually involves a trial of an extensively hydrolysed formula first unless symptoms are severe and if extensively hydrolysed formulas fail, in which case an amino acid formula must be trailed. Amino acid formulas are used first line in infants who are breastfed and who require top-up feeds. Soya formulas are not recommended in children under 6 months of age.

Lactose Intolerance vs Cow’s Milk Allergy – The Symptoms

Lactose intolerance does not involve the immune system and does not cause immediate symptoms. Please see the table below which illustrates the symptoms of lactose intolerance and non-IgE cow’s milk allergy.

Benefits of Lactose

  • Gut Health

One study shows that in infants, the addition of lactose in baby formula, results in an increase in Bifidobacteria and Lactobacilli (good bacteria), and a decreased number of Bacteroides and Clostridia (bad bacteria) compared to a lactose-free variant (9). The same study also demonstrates a positive effect of added lactose on the microbiome with increased concentrations of butyrate, a short-chain fatty acid (SCFA). SCFA’s are an important fuel for intestinal epithelial cells and are known to strengthen the gut barrier function and have an important immunomodulatory function (10).

  • Enhanced Calcium Absorption

Formulas that contain lactose have been shown to significantly increase the absorption of calcium, including other minerals also such as magnesium (11, 12)

  • Palatability

Extensively hydrolysed formulas (eHF) that contain lactose are sweeter and more palatable in comparison to those without lactose in. eHF are used in the management of cow’s milk allergy and can be strong and bitter in taste (13).

Comparison of Lactose Intolerance vs non IgE Cow’s Milk Allergy

To bring it all together, please see the table 3 which compares and contrasts LI to non-IgE CMA:


Because lactose intolerance in children under 5 years of age is rare, lactose intolerance is most likely secondary to mucosal injury, resulting from either a gastro-intestinal illness or enteropathy such as non-IgE mediated cow’s milk allergy.

Due to the many benefits of lactose (supports the microbiome, enhances calcium absorption, and enhances the palatability of infant formula), it is recommended not to eliminate lactose for longer than required. For infants with loose stools, a lactose-free formula may be required at first but not for longer than 6 weeks. If no resolution is seen, consider CMA.

Here at Nishti’s Choice we provide expert help and advice to families with an allergy baby. To book a no-obligation chat please visit the booking page.


  • Heine RG, AlRefaee F, Bachina P, et al. Lactose intolerance and gastrointestinal cow’s milk allergy in infants and children – common misconceptions revisited. World Allergy Organ J. 2017;10(1):41. Published 2017 Dec 12. doi:10.1186/s40413-017-0173-0
  • Martin CR, Ling PR, Blackburn GL. Review of Infant Feeding: Key Features of Breast Milk and Infant Formula. Nutrients. 2016;8(5):279. Published 2016 May 11. doi:10.3390/nu8050279
  • Skovbjerg H, Norén O, Sjöström H, Danielsen EM, Enevoldsen BS. Further characterization of intestinal lactase/phlorizin hydrolase. Biochim Biophys Acta. 1982;707(1):89-97. doi:10.1016/0167-4838(82)90400-9
  • Tan-Dy CR, Ohlsson A. Lactase treated feeds to promote growth and feeding tolerance in preterm infants. Cochrane Database Syst Rev. 2013;2013(3):CD004591. Published 2013 Mar 28. doi:10.1002/14651858.CD004591.pub3
  • Rasinperä H, Savilahti E, Enattah NS, et al. A genetic test which can be used to diagnose adult-type hypolactasia in children. Gut. 2004;53(11):1571-1576. doi:10.1136/gut.2004.040048
  • Walsh J, Meyer R, Shah N, Quekett J, Fox AT. Differentiating milk allergy (IgE and non-IgE mediated) from lactose intolerance: understanding the underlying mechanisms and presentations. Br J Gen Pract. 2016;66(649):e609-e611. doi:10.3399/bjgp16X686521
  • Fiocchi A, Brozek J, Schünemann H, et al. World Allergy Organization (WAO) Diagnosis and Rationale for Action against Cow’s Milk Allergy (DRACMA) Guidelines. World Allergy Organ J. 2010;3(4):57-161. doi:10.1097/WOX.0b013e3181defeb9
  • Venter C, Brown T, Shah N, Walsh J, Fox AT. Diagnosis and management of non-IgE-mediated cow’s milk allergy in infancy – a UK primary care practical guide. Clin Transl Allergy. 2013;3(1):23. Published 2013 Jul 8. doi:10.1186/2045-7022-3-23
  • Francavilla R, Calasso M, Calace L, et al. Effect of lactose on gut microbiota and metabolome of infants with cow’s milk allergy. Pediatr Allergy Immunol. 2012;23(5):420-427. doi:10.1111/j.1399-3038.2012.01286.x
  • Parada Venegas, D., K., M., Landskron, G., González, M. J., Quera, R., Dijkstra, G., Harmsen, H. J., Faber, K. N., & Hermoso, M. A. (2019). Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases. Frontiers in Immunology, 10, 424615.
  • Ziegler EE, Fomon SJ. Lactose enhances mineral absorption in infancy. J Pediatr Gastroenterol Nutr. 1983;2(2):288-294.
  • Abrams SA, Griffin IJ, Davila PM. Calcium and zinc absorption from lactose-containing and lactose-free infant formulas [published correction appears in Am J Clin Nutr 2002 Nov;76(5):1142]. Am J Clin Nutr. 2002;76(2):442-446.
  • Miraglia Del Giudice M, D’Auria E, Peroni D, et al. Flavor, relative palatability and components of cow’s milk hydrolysed formulas and amino acid-based formula. Ital J Pediatr. 2015;41:42. Published 2015 Jun 3. doi:10.1186/s13052-015-0141-7
  • Heine RG. Pathophysiology, diagnosis and treatment of food protein-induced gastrointestinal diseases. Curr Opin Allergy Clin Immunol. 2004;4(3):221-229. doi:10.1097/00130832-200406000-00015