Infant allergy, unsettled behaviour, and the gut: PLAIN LANGUAGE SUMMARY for health professionals
Unsettled infant problems and the effects of allergy on the gut
True allergy in an infant, toddler or older child can be a serious condition which requires parental vigilance and careful monitoring. However, allergy and intolerance — most especially cow’s milk allergy or intolerance — is overdiagnosed and overtreated(1) in infants and toddlers.
There is a common concern that an infant’s sleep problems may be attributable to allergy or wind pain, or that allergy and gut dysbiosis cause the infant to ‘dial up’ or cry, thereby interfering with sleep. The evidence does not support this. Eliminating various foods from a breastfeeding mother’s diet will not help a breastfed infant to be more settled. The only form of allergy which might cause disrupted sleep in infants is a very extensive skin rash or eczema,(2) which could cause waking due to irritation and itchiness.
Prescribing unnecessary elimination diets(3) increases the likelihood that the infant will develop an allergy later on. This is because exposure to a low dose of a food protein (which occurs through breast milk) in the early months of life primes the immune system and stimulates tolerance to that food protein. Infants and toddlers benefit from exposure to the wide range of foods found in the parental diet, whether through breast milk or once solids are being introduced.(4)
Green stools and mucous in the stool are not signs of worrying inflammation, allergy, lactose overload, gut dysbiosis or gut problems. Frequency and consistency of infant stools often vary within the same infant, and this changeability is more pronounced with the introduction of solids. Blood in the stool warrants medical review, as do any concerns about the infant’s health. Blood in the stool is addressed here.
Allergy is often overdiagnosed and overtreated in infants
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Cow’s milk allergy is the most common allergy in infants and toddlers, but occurs only occasionally(5) and continues to be very commonly overdiagnosed and overtreated.(6)
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Cow’s milk allergy is the only form of allergy that has been linked(7) with excessive crying in the first 16 weeks of life (a distinct clinical presentation from patterns of excessive night waking in the first 12 months of life).
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Soy, egg, and grain protein allergies may occur in infants and toddlers, but also very uncommonly,(8) and are similarly often overdiagnosed. They do not cause sleep or crying problems.
Breastfed infants and cow’s milk allergy
Even a diagnosis of true cow’s milk allergy(9) in a breastfed infant or toddler does not require cessation of breastfeeding,(10) nor commencement of a maternal dairy elimination diet(11) (except in extremely rare circumstances(12)).
Cow’s milk proteins usually do not occur at high enough levels in breast milk to trigger allergic reactions in infants, regardless of how much dairy the mother consumes. When a breastfeeding mother follows a dairy elimination diet:
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There is a greater chance the infant will develop a cow’s milk allergy later.(13)
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The mother loses the nutritional benefits of dairy (including calcium and vitamin D) and possible enjoyment(14) benefits of dairy foods.
For formula-fed infants(15) diagnosed with a true cow’s milk allergy, a specialised formula(16) may be required.
Types of cow’s milk allergy
There are two main types of cow’s milk allergy.(17)
IgE-mediated cow’s milk allergy
An infant with an IgE-mediated cow’s milk allergy may present with one or more of the following:
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Skin rashes (urticaria, eczema(18))
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Hayfever(19)
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Reactive airways
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Vomiting(20) within two hours of ingesting infant formula or a dairy product
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Anaphylaxis (which is life-threatening).
Non-IgE-mediated cow’s milk allergy
An infant with a non-IgE-mediated cow’s milk allergy may present with one or more of the following:
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Constipation(21)
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Significant and recurring amounts of blood(22) in the stool, also referred to as food protein induced allergic proctocolitis.(23) (Most infants with streaks or specks of blood in the stool do not have cow’s milk allergy, and the flecks usually disappear within a month or so.(24))
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Food protein-induced enterocolitis syndrome(25)
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Anaphylaxis (which is life-threatening).
None of these conditions causes a pattern of excessive night waking(26) in infants, nor causes an infant to fuss at the breast or bottle. A pattern of excessive night waking is typically caused by a disrupted body clock and is addressed through evidence-based sleep management approaches such as The Possums Sleep Program. It can be reassuring for parents to understand that an infant’s or toddler’s disrupted sleep and fussy behaviour is not caused by gut pain or allergy, despite prevalent reports to the contrary.
Footnotes
Please see the related resources listed at the bottom of this page for links to comprehensive analyses of the research literature, citations, and the NDC clinical guidelines on these topics.
(1) There is an international trend to overdiagnosis and overtreatment, including in infants and children. This is not only expensive for health systems, but brings a whole range of unexpected and unintended effects.
(2) A severe eczema may be considered to be allergic only after it does not resolve with topical steroids and there is a history of sensitisation to cow’s milk protein (that is, exposure to formula).
(3) Whether by asking a breastfeeding mother to eliminate foods or by eliminating foods from the small child’s diet as solids are introduced.
(4) If the infant is fussing and arching the back during breastfeeds, this most likely signals underlying problems with fit and hold, resulting in an unstable feeding position. This problem is often misdiagnosed as a sign of allergy. Support from an NDC Accredited health professional, applying the gestalt method to help with positional instability, is recommended (see https://ndcinstitute.au/find-an-ndc-practitioner). If the infant is fussing and arching the back during bottle feeds, paced bottle feeding should be reviewed. Sometimes infants develop a conditioned dialling up with the breast or bottle, which is also often misdiagnosed as allergy.
(5) Prevalence is estimated at 0.4%–0.8% in exclusively breastfed infants prior to introduction of any breast milk substitutes or solid foods; in about 2% of infants otherwise.
(6) Allen et al 2022 developed a Delphi consensus statement, drawing on experts who did not have a conflict of interest with formula companies, to explain circumstances in which the diagnosis of cow’s milk allergy is useful or necessary.
(7) Although cow’s milk allergy can be relevant when infants cry and fuss excessively in the first 16 weeks of life, CMA is also commonly overdiagnosed in crying infants. Also, the research linking CMA with excessive crying does not take into account resolvable factors which result in dialled up infants or the behaviours which are often misdiagnosed as due to allergy.
(8) The prevalence of these and other food allergies remains poorly established.
(9) Including food protein induced enteropathy syndrome.
(10) The only absolute medical contraindication to breastfeeding or use of donor breastmilk is classic galactosaemia.
(11) A study by Munblit et al 2020 documented the influence of formula-producing pharmaceutical companies on development of clinical guidelines concerning infant cow’s milk allergy. The authors found that more than 99% of infants and toddlers with true cow’s milk allergy are likely to tolerate breast milk from a woman who is consuming dairy products, without having an allergic reaction. McWilliam et al 2023 conclude that concentrations of cow’s milk proteins in breast milk vary widely, irrespective of the amounts consumed by the mother and the timing of consumption, with beta lactoglobulin (a cow’s milk protein) detected in about half of samples regardless of cow’s milk consumption. It is difficult to consume enough dairy for beta lactoglobulin to reach a significant level in breast milk. Even in the case of a true cow’s milk allergy, maternal elimination diet should not be a standard recommendation for breastfeeding infants. If maternal elimination diet is indicated, Allen et al 2022 state that goat and sheep milk protein should also be avoided due to cross-reactivity, and that re-introduction would occur if a two-week trial does not result in resolution of symptoms, or two weeks after symptoms have resolved.
(12) This is the situation of an exclusively or partially breastfed infant who becomes sick with a protein-losing enteropathy, presenting with faltering growth and low serum albumin, with or without oedema.
(13) McWilliam et al 2023.
(14) Of course, this is not relevant if the breastfeeding woman is lactose or cow’s milk protein intolerant herself, and avoids cow’s milk protein for that reason.
(15) Cross-reactivity between cow’s milk and soy-based formulas is low, so infants with cow’s milk allergy and food protein induced enteropathy syndrome who are over six months of age could use soy-based formula.
(16) Specialised formulas include extensively hydrolysed formula, amino acid formula, and soya or rice-based formulas. Mehta et al 2022 demonstrate that volumes of specialised formula prescriptions have increased two-fold in the past twenty years in the UK, Australia and Norway, in the absence of increased prevalence of milk allergy. They propose that most infants prescribed specialised formula do not have milk allergy. They identify up to a ten-fold excess prescription rate relative to the true rate of milk allergy. The authors observe that unnecessary specialised formula use increases consumption of free sugars (such as glucose or sucrose, which substitute for the lactose found in breast milk and formula), risking dental decay and obesity in later life.
(17) It is also possible to have a mixed non-IgE and IgE cow’s milk allergy. Coeliac disease and cow’s milk-induced iron deficiency anaemia may be included in the category of non-IgE mediated cow’s milk allergy.
(18) Eczema is not usually due to cow’s milk allergy. There has been a tendency to overdiagnose cow’s milk allergy as a cause of eczema. Only a very extensive eczema may be related to cow’s milk allergy.
(19) Allergic rhinitis.
(20) This may be accompanied by swelling (angioedema), urticaria, respiratory symptoms, and erythema; symptoms resolve within a few hours. These are signs of a serious medical condition requiring urgent medical attention. These immediate-onset symptoms occur each time there is direct ingestion of cow’s milk protein. Depending on the age of the infant, they will be accompanied by a positive skin prick test or serum IgE.
(21) Most constipation is not cow’s milk allergy. Breastfed infants may not pass stool for many days at a time; as long as the infant is gaining weight well, this is of no clinical concern. Constipation and a true gastro-oesophageal reflux disease in an older child may be classified as food protein-induced dysmotility disorders.
(22) Blood in the stool is referred to medically as haematochezia.
(23) Infants may have regular small spots of blood in the stool, which are not of concern and are diagnosed as non-allergic benign infant proctocolitis. Food protein induced allergic proctocolitis (FPIAP) is a delayed non-IgE or cell-mediated food allergy. It presents with haematochezia in otherwise well infants, often in the first month or two of life, and usually does not occur after the first year of life. Breast milk fed infants, whether exclusively or partly, have a lower risk of developing FPIAP compared to those fed only formula. FPIAP is not associated with vomiting, diarrhoea or failure to thrive; these are signs of food-protein-induced enteropathy syndrome. If the infant is formula fed and has daily visible blood in the stools, extensively hydrolysed formula is likely to be advised. If the infant is breastfed and the haematochezia is mild, observation for a two-month period is recommended, as FPIAP is less common than previously believed among infants with symptoms of proctocolitis (or haematochezia) and may even be due to viral infection (Arvola et al 2006; McWilliam et al 2023). The term non-allergic benign infantile proctocolitis has been recommended for this harmless form of blood in the stool (Gelsomino et al 2021). If haematochezia persists, or is moderate to severe, the infant is diagnosed with food-protein-induced allergic proctocolitis and a maternal cow’s milk elimination diet is required.
(24) A wait-and-watch approach is appropriate for the first two months in infants with haematochezia, as long as the amount of bleeding remains just a streak or drop of blood in the nappy only.
(25) Food protein induced enteropathy syndrome (FPIES) occurs predominantly in formula-fed infants. It is rare in breastfed infants but can occur, for example, when a breastfed infant is fed formula or commences solids containing cow’s milk protein. Acute FPIES presents as vomiting one to four hours after a feed, with pallor, sweatiness and clamminess, hypotonia, lethargy, diarrhoea, and hypovolaemia (shock). An infant with FPIES is very unwell and requires emergency care. Chronic FPIES presents with intermittent vomiting, frequent diarrhoea, abdominal distension, pallor after feeds, hypotonia, lethargy, dehydration, failure to thrive, and hypovolaemia. Chronic FPIES is also a serious medical condition requiring prompt or urgent medical care. There is no validated diagnostic test for FPIES.
(26) Unless the infant is acutely unwell with FPIES requiring urgent medical care.
Related resources
Infant allergy, unsettled behaviour, and the gut: PLAIN LANGUAGE SUMMARY for health professionals
Infant haematochezia (blood in the stool): PLAIN LANGUAGE SUMMARY for health professionals
Haematochezia and allergy in the breastfed infant. Dr Pamela Douglas 12 June 2024 - VIDEO
NDC clinical guidelines: Haematochezia and allergy in the breastfed infant POWERPOINT.pdf
For parents
It's normal for babies to have green stools and mucous in the stool
Is your baby unsettled or having trouble sleeping because of allergy?
Does allergy cause toddler sleep problems?
Infant cow's milk protein allergy (parent handout) available under possums.org Free Resources
Selected references
Abrams EM, Shaker MS, Chan ES. Prevention of food allergy in infancy: the role of maternal interventions and exposures during pregnancy and lactation. The Lancet Child and Adolescent Health. 2023;7:358-366.
Allen HI, Wing O, Milkova D. Prevalence and risk factors for milk allergy overdiagnosis in the BEEP trial cohort. Food Allergy and Gastrointestinal Disease. 2024;80:148-160. DOI: 110.1111/all.16203.
Bhasin M, Cooper M, Macchiaverni P. Colostrum as a protective factor against peanut allergy: evidence from a birth cohort. Allergy. 2025:1–11. https://doi.org/10.1111/all.70043.
Buccini G, Larrison C, Neupane S, et al. Complex intertwined association between breastfeeding practices and household food insecurity: Systematic review and meta-analysis. Matern Child Nutr. 2024;20(4):e13696. doi:10.1111/mcn.13696
Caffarelli C, Giannetti A, Buono EV. Cow's milk allergy in breastfed infants: what we need to know about mechanisms, management, and maternal role. Nutrients. 2025;17(1787):https://doi.org/10.3390/nu17111787.
Ding Y, Zhu C, Li S, et al. Breastfeeding and risk of food allergy and allergic rhinitis in offspring: a systematic review and meta-analysis of cohort studies. Eur J Pediatr. 2024;183(8):3433-3443. doi:10.1007/s00431-024-05580-w
Fleischer DM, Chan ES, Venter C. A consensus approach to the primary prevention of food allergy through nutrition: guidance from the American Academy of Allergy, Asthma, and Immunology; American College of Allergy, Asthma, and Immunology; and the Canadian Society of Allergy and Clinical Immunology. American Academy of Allergy, Asthma & Immunology. 2020:https://doi.org/10.1016/j.jaip.2020.1011.1002.
Hage G, Sacre Y, Haddad J. Food hypersensitivity: distinguishing allergy from intolerance, main characteristics, and symptoms - a narrative review. Nutrients. 2025;17:1359. https://doi.org/1310.3390/nu17081359.
Munblit D, Perkin MR, Palmer D, Allen K, Boyle RJ. Assessment of evidence about common infant symptoms and cow's milk allergy. JAMA Pediatrics. 2020;174:599-608.