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What Is Milk Soy Protein Intolerance?

What Is Milk Soy Protein Intolerance?
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Updated on April 28, 2025
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Milk soy protein intolerance (MSPI) is a temporary inability to digest the proteins in either cow’s milk, soy milk, or both, which typically affects infants. It’s also referred to as cow’s milk protein intolerance, and it’s different than a milk allergy.

Allergic colitis is the most common symptom of MSPI.

Allergic colitis can cause inconsolable crying and bloody stool in infants. While this can feel intense and be scary for parents, MSPI is treatable through dietary changes and is temporary in most children, often fading by the baby’s first birthday.

Signs and Symptoms of Milk Soy Protein Intolerance

MSPI symptoms usually appear in the infant’s first few weeks or months of life.

 Symptom intensity can vary based on how sensitive they are to a specific food protein. Some babies may have severe reactions, while others only show mild symptoms.

Illustrative graphic titled Signs and Symptoms of Milk Soy Protein Intolerance shows Vomiting, Diarrhea, Weight Loss or Not Gaining Weight, Nasal Congestion, Gas, Bloating, or Belly Pain, Acid Reflux, Rash or Eczema, Blood or Mucus in Stool,

MSPI signs and symptoms usually appear during an infant’s first few months of life, and they range from mild to severe.

Everyday Health
MSPI symptoms include:

  • Vomiting
  • Diarrhea
  • Weight loss or trouble gaining weight
  • Nasal congestion
  • Gas and bloating
  • Abdominal pain
  • Acid reflux
  • Rashes or eczema
  • Blood or mucus in stool
It’s also common for babies with MSPI to show signs of colic, or inconsolable crying. Infants with MSPI may:

  • Cry for up to 18 hours per day
  • Refuse to breastfeed or take a bottle
  • Overeat or seem more hungry than usual
  • Seem irritable or fussy
Delayed reactions to milk or soy protein can also occur, making it harder to figure out what’s causing your baby’s symptoms.

Food Intolerance vs. Food Allergy

Food intolerances and food allergies are different things, with two distinct meanings. While allergies involve the immune system, an intolerance means the body can’t digest a food for reasons other than an immune response, such as lacking necessary digestive enzymes.

Allergies also fall into two categories:

  • IgE-mediated: This type involves allergic reactions that show up quickly and involve the antibody IgE.
  • Non-IgE-mediated: These types of inflammatory reactions still involve the immune system, but not the IgE antibody. Non-IgE-mediated reactions take longer to show up and tend to be related to digestion. Most milk protein allergies and cases of MSPI fall into this category.
MSPI is not a cow’s milk allergy or a soy allergy, and its symptoms may take longer to appear.

Allergic Colitis

Allergic colitis occurs when a certain protein allergy causes inflammation in the colon. Symptoms may include:

  • Blood or mucus in stool
  • Gas
  • Abdominal pain
  • Diarrhea
  • Vomiting

MSPI in Adults

“While MSPI is primarily diagnosed in infants, adults can experience non-IgE-mediated sensitivities to milk or soy proteins,” says David Kahana, MD, a gastroenterologist and 1MD Nutrition Advisory Board member.

Dr. Kahana says that people often mistake these sensitivities for irritable bowel syndrome, as symptoms typically include bloating, abdominal pain, diarrhea, and fatigue.

Adult-onset cow’s milk protein allergies — although rare — are also more likely to be IgE-mediated, or similar to a classic allergic reaction.

Causes and Risk Factors of Milk Soy Protein Intolerance

An intolerance to milk or soy can sometimes run in families, although any baby can develop MSPI.

 Infants with a family history of allergies or asthma may also be more likely to develop food intolerances and allergic colitis.

Foods that could trigger a reaction in someone with a cow’s milk protein intolerance include all dairy products, such as:

  • Cow’s milk
  • Half-and-half
  • Cream
  • Yogurt
  • Butter
  • Ice cream
  • Cheese
  • Whey
  • Cottage cheese
  • Sour cream
  • Condensed or evaporated milk

Meanwhile, these foods could trigger a reaction in those with soy protein intolerance:

  • Tofu
  • Edamame or soybeans
  • Soy milk
  • Soy sauce
  • Miso
  • Soy protein isolate
  • Tempeh
  • Textured vegetable protein
  • Soy flour
  • Soy-based dairy or meat alternatives
Soy lecithin and refined soybean oil are usually safe for infants with MSPI because the refining process separates these products from the soy protein, but they could still cause a reaction in someone with high sensitivity.

If a breastfeeding infant is experiencing symptoms, it may be due to the mother’s diet, as some proteins can remain in breastmilk. The mother can try cutting out milk, soy, or both from her diet to see if there’s improvement in the baby’s symptoms.

Infant formulas can also contain dairy or soy protein. There are nondairy and soy-free options available.

How Is Milk Soy Protein Intolerance Diagnosed?

MSPI is a clinical diagnosis, so doctors will watch for symptoms in response to different foods, says Kahana. “If symptoms improve after removing milk and soy proteins from the infant’s or breastfeeding mother’s diet and return upon reintroduction, that pattern is usually considered diagnostic,” he says.

Doctors might also perform stool tests to determine if there’s blood or evidence of a reaction.

In rarer cases, an endoscopy, a procedure using a small camera to view the inside of the body, could help reveal inflammation.

Doctors may also try to rule out other similar conditions, such as:

  • Food allergies
  • Celiac disease
  • Inflammatory bowel disease
  • Lactose intolerance
  • Anal fissures
  • Intussusception, a condition where the intestine folds over itself
  • Infectious colitis, or inflamed colon due to infection
  • Necrotizing enterocolitis, a life-threatening condition causing gut inflammation and infection

Treatment

The main treatment for MSPI and allergic colitis is identifying and eliminating triggering foods and allowing the colon to heal from any remaining inflammation.

“Specific probiotics may support gut health and reduce inflammation in infants with disrupted gut microbiota or a family history of allergic conditions,” Kahana says.

Prevention of Milk Soy Protein Intolerance

“There is no guaranteed way to prevent MSPI, but certain practices may help reduce the risk,” says Kahana. These include avoiding unnecessary antibiotics, consuming a diverse diet during pregnancy, and supporting the microbiome early in life through breastfeeding.

Still, treatment is usually straightforward once you know which foods cause a reaction. Preventing flare-ups involves vigilantly keeping the triggering food — whether dairy, soy, or both — out of your diet.

Lifestyle Changes for Milk Soy Protein Intolerance

“Consistency is critical when managing MSPI,” says Kahana. “Even trace amounts of milk or soy proteins can trigger symptoms, so it’s essential to follow a strictly controlled diet and carefully monitor all ingredients.”

Many food additives contain dairy or soy, so it can be difficult to tell if a food contains these allergens from reading the ingredients. A good rule of thumb is to check the label for “may contain dairy” or “may contain soy,” and avoid foods with this warning.

Breastfeeding

If you’re breastfeeding an infant with MSPI, you’ll need to eliminate all trigger foods from your diet, since milk and soy proteins pass through breastmilk.

 It can take up to two weeks for these proteins to clear from your milk supply, so it may take that long to see symptoms improve.

Your doctor may recommend switching to a hypoallergenic formula for the time it takes your body to clear the allergens (and pumping to keep up your milk supply) before resuming breastfeeding.

Formula-Feeding

Switching to hypoallergenic formulas, such as protein hydrolysate, or amino acid–based formulas, which break down proteins into smaller pieces for easier digestion, can help infants with MSPI.

Solid Foods

Work with your pediatrician to decide when to introduce solid foods to a baby with MSPI. It may be recommended that you wait until 6 months of age to start solid foods and then introduce foods in a slightly different order than in babies without MSPI.

How Long Does Milk Soy Protein Intolerance Last?

For most infants, MSPI resolves by their first birthday.

It can take time for the colon to recover from allergic colitis after removing the triggering foods. You might notice a more immediate improvement in your infant’s appetite and mood, but it can take up to three or four weeks to stop seeing bloody stool as the allergic colitis heals.

Complications of Milk Soy Protein Intolerance

Untreated MSPI can lead to chronic gut inflammation, difficulty gaining weight, nutrient deficiencies, anemia, and in severe cases, protein-losing enteropathy, a condition that causes too much protein to leak from the digestive tract, Kahana says.

Infants with untreated MSPI could also experience more irritability, sleep disruptions, and failure to thrive, says Kahana. “Early diagnosis and proper management are essential to avoid these complications and support healthy development,” he says.

Research and Statistics: Who Has Milk Soy Protein Intolerance?

MSPI overwhelmingly affects infants under age 1.

 While there hasn’t been much research on the prevalence of MSPI, it’s uncommon — and only 2 to 3 percent of infants have a cow’s milk allergy and allergic colitis.

Up to half of infants with a cow’s milk intolerance also develop soy intolerance.

Research suggests that food protein–induced allergic colitis is responsible for bloody stool in over 60 percent of children with this symptom.

Related Conditions

Some conditions involving food intolerances or allergies are similar to MSPI, including:

  • Food protein–induced enterocolitis syndrome: This condition causes an immune reaction to foods including milk, soy, rice, oats, eggs, and seafood. Common symptoms include diarrhea and vomiting.

  • Gastroesophageal reflux disease: This is chronic acid reflux that can involve nausea, heartburn, and asthma-like symptoms.

  • Eosinophilic gastroenteritis: This condition causes inflammation in different parts of the digestive tract related to the immune response.

Some evidence suggests that infants with allergic colitis could have a higher risk of developing conditions such as eczema, asthma, and food allergies later in life, especially if they have a strong family history of allergies, says Kahana.

Kahana adds that research on the connection between chronic inflammatory bowel diseases like allergic colitis and conditions like Crohn’s disease and ulcerative colitis is still uncertain and in progress.

The Takeaway

  • MSPI is an intolerance to cow’s milk and soy proteins. While it’s not the same thing as an allergy, people often use these words interchangeably.
  • Allergic colitis is a symptom of MSPI, and it mostly affects infants.
  • Vomiting, diarrhea, rashes, extreme fussiness, and bloody stool are common signs of MSPI and allergic colitis.
  • Eliminating trigger foods is the main method for treating MSPI, but this condition also tends to resolve on its own by the child’s first birthday.

Common Questions & Answers

What are the symptoms of MSPI?
The symptoms of MSPI are the same as those of allergic colitis. They include vomiting, diarrhea, weight loss, reflux, skin rashes, and bloody stool. In infants, this can come with inconsolable crying, or colic.
It’s possible to have only an intolerance to milk protein, in which case you’d be able to eat soy without any digestive symptoms. However, soy protein intolerances commonly appear alongside milk protein intolerances, so it’s a good idea to consider whether soy could also be triggering symptoms if you already have an intolerance to dairy.
Both soy and cow’s milk intolerances can cause allergic colitis, so the baby’s poop (stool) will look similar regardless of the specific food that’s triggering the reaction. Allergic colitis can cause the baby’s poop to contain flecks or streaks of bright red blood, as well as mucus. It can also cause loose, watery stools or diarrhea.

Resources We Trust

EDITORIAL SOURCES
Everyday Health follows strict sourcing guidelines to ensure the accuracy of its content, outlined in our editorial policy. We use only trustworthy sources, including peer-reviewed studies, board-certified medical experts, patients with lived experience, and information from top institutions.
Resources
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Jon E. Stahlman, MD

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Jon E. Stahlman, MD, has been a practicing allergist for more than 25 years. He is currently the section chief of allergy and immunology at Children’s Healthcare of Atlanta's Scottish Rite campus and the senior physician at The Allergy & Asthma Center in Atlanta. He served as the president of the Georgia Allergy Society, has been named a Castle Connolly Top Doctor, and was listed as a Top Doctor by Atlanta magazine. His research interests include new therapies for asthma and allergic rhinitis as well as the use of computerized monitoring of lung function.

He received his bachelor's and medical degrees from Emory University. He completed his pediatric residency at Boston Children’s Hospital and his fellowship in allergy and clinical immunology at Harvard University’s Boston Children’s Hospital and Brigham and Women’s Hospital. After his training, Dr. Stahlman conducted two years of clinical research at Boston Children’s Hospital and was part of the faculty at Harvard Medical School, where he taught medical students and allergy and immunology fellows.

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