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What is the difference between lactose malabsorption, lactose intolerance, and lactose overload?

Dr Pamela Douglas9th of May 20259th of May 2025

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What is lactose malabsorption?

Lactose malabsorption doesn't always result in the signs and symptoms of lactose intolerance

When there is lactose malabsorption, undigested lactose comes into contact with the microbiota in the colon, which ferment the lactose. Lactose malabsorption has multiple causes, in both infants and adults.

What is lactose intolerance?

Multiple factors influence the development of symptoms related to lactose malabsorption. These extrinsic factors include the amount of lactose ingested, other foods which affect intestinal transit, and the rate of lactose delivery to the colon. When signs and symptoms are experienced, the individual is diagnosed with lactose intolerance.

  • In adults the amount of gas production from lactose malabsorption correlates with presence and severity of intestinal symptoms.

  • Diarrhoea will result if the respective load of lactose exceeds the capacity of the colonic microbiota for fermentation or the SCFA load exceeds the colon capacity for resorption.

  • The signs of abdominal pain, borborygmi (rumbling tummy), and bloating correlate with increased hydrogen gas found in breath tests.

Lactose malabsorption, lactose intolerance, and infancy

There are three kinds of lactose malabsorption which may become clinically relevant lactose intolerance in infants.

1. Congenital lactase deficiency is a rare life-threatening condition in newborns

Congenital lactase deficiency is an extremely rare, autosomal recessive condition which results in complete lactase absence. This causes severe symptoms in the newborn, and life-threatening failure to thrive.

The elevated osmolality of lactose passing through the gut without hydrolysis in the small intestine results in severe osmotic diarrhoea, hyperosmolar dehydration, abdominal bloating and pain, impaired glucose absorption, and gastroenteritis or mucosal damage.

2. Secondary lactose intolerance

In infants, gastroenteritis or severe cow's milk protein intolerance may cause reduced lactase activity and lactose malabsorption, resulting in frequent diarrhoea. However, this is transitory, as the endocytes regenerate after a period of time.

  • Rotavirus infection seems to increase lactose malabsorption in infants.

  • Secondary lactose malabsorption with signs of lactose intolerance is not a reason to stop breastfeeding.

  • If the infant is already taking formula and has signs of persisting secondary lactose intolerance subsequent to gastroenteritis or severe cow's milk allergy, the formula should be changed to lactose-free formula.

3. Lactose overload in the breastfed or breast milk fed infant

Concerns that a breastfed infant may be experiencing lactose intolerance, referred to in breastfed infants as lactose overload, is not an indication to order a ‘hydrogen breath test’ or test for ‘reducing sugars’ in the stool.

  • Both these tests are positive in most normal breastfed babies in the first few months of life.

  • Stool reducing substances (ie. unabsorbed reducing sugars) in infant stool are not linked to the occurrence of colic. The presence of reducing substances in the stool of infants fed human milk is four times higher than that of formula fed infants, probably due to the presence of a substantial amount of HMO.

  • Similarly, faecal calprotectin is elevated in breastfed infants, and highly variable. Testing for faecal calprotectin is not indicated in unsettled infants or breastfed babies who are showing signs of lactose overload.

  • Unfortunately, these tests may exacerbate anxiety, but don't help diagnose lactose overload.

If the baby is breastfed and has a true lactose overload, or has had a gastroenteritis and is currently lactose intolerant, there is no reason to stop breastfeeding, as breastmilk promotes regeneration of the small gut endothelium and is anti-inflammatory.

Lactase non-persistence results in primary lactose malabsorption after about three years of age

Lactase persistence is an inherited trait which occurs in only 30% of the world’s population, though the prevalence varies between populations and ethnicities.

Lactase non-persistence is characterised by a gradual decline in lactase level during maturation. It results in a primary lactose malabsorption, which leads to an increased concentration of lactose in the colon.

Traditionally, cultures that have relied on pastoralism and dairy products in the past exhibit higher prevalence of lactase persistence than populations with little dairy consumption. Lactase non-persistence is not a disease, but a genetic wildtype.

Lactose intake does not affect lactase production or activity. Withdrawing lactose from the diet does not reduce intestinal lactase expression.

Not all adults with lactase non-persistence experience lactose intolerance

Only some lactase-deficient individuals experience gastrointestinal symptoms such as bloating, diarrhoea, flatulence, and abdominal pain, diagnosed as lactose intolerance. Many lactose malabsorbers tolerate certain amounts of dietary lactose without symptoms.

The lactose non-persistence geneotype is associated with higher Bifidobacteria levels when lactose is ingested (known as the bifidogenic effect).

Lactobacillus and Bifidobacterium adapt to the presence of lactose into the colonic lumen, resulting in increased tolerance. In lactase-deficient individuals, lactose feeding supports the growth of lactose-digesting bacteria in the colon, which enhances colonic lactose processing and possibly reduces intolerance symptoms. This process is known as colonic adaptation.

The faecal bacteria of lactose intolerant subjects generate fermentation end products in response to lactose faster than those of the tolerant group. Together with undigested lactose, the rapid accumulation of fermentation products increases the osmotic load in the colonic lumen, resulting in diarrhoea.

When colonic microbes produce the hydrogen via the fermentation process, breath hydrogen concentration rises and can be measured. Breath hydrogen is not a clinically useful test in infants who have a lactose overload: other signs are more useful.

Recommended resources

Is your baby unsettled or having trouble sleeping because of lactose?

Lactose: mammary gland synthesis and secretion + digestion in the infant gut

Lactose: your breastmilk and your baby depend upon it

Limitations of the hypothesis that lactose back-defusion from 'hyperlactation' decreases breastmilk production and causes breast inflammation

Two six-week-old breastfed babies with severe functional lactose overload of breastfeeding + what happened next

Selected references

Forsgard RA. Lactose digestion in humans: intestinal lactase appears to be constitutive whereas the colonic microbiome is adaptable. American Journal of Clinical Nutrition. 2019;110:273-279.

Misselwitz B, Butter M, Verbeke K, Fox MR. Update on lactose malabsorption and intolerance: pathogenesis, diagnosis and clinical management. Gut. 2019;68:2080-2091.

Sadovnikova A, Garcia SC, Hovey RC. A comparative review of the extrinsic and intrinsic factors regulating lactose synthesis. Journal of Mammary Gland Biology and Neoplasia. 2021;26(197-215).

Sadovnikova A, Garcia SC, Hovey RC. Comparative review of the cell biology, biochemistry, and genetics of lactose synthesis. Journal of Mammary Gland Biology and Neoplasia. 2021;26(181-196).

Toca MdC, Fernandez A, Orsi M, Tabacco O, Vinderola G. Lactose intolerance: myths and facts. An update. Archivos Argentinos de Pediatria. 2022;120(1):59-66.

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