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Choosing the right formula can feel daunting for any parent, but when your baby has severe allergies, intolerance issues, or GI conditions, you’ll need to make your choice very carefully. About 80% of the formulas on the market are made with cow’s milk. All babies under 1 

lack the ability to digest cow’s milk properly, which is why formula companies alter the milk proteins in their products in a way that makes the formula safe for babies to have. 

But for babies with an allergy or intolerance to dairy, this process isn’t enough to make the formula digestible. Fortunately, there are hypoallergenic options made with milk proteins that are broken down into much smaller parts so your baby’s digestive system doesn’t have to do the work. 

Formula Options for Babies With an Intolerance

Babies with an intolerance to milk may have a lot of discomfort and gassiness when they have standard formulas, but these aren’t true allergies. An intolerance involves only the digestive system and not the immune system. 

Soy formula. For some babies, a soy-based formula can be a stand-in for cow’s milk-based options. But talk to your pediatrician – soy is also a common allergen, so this option is not considered hypoallergenic.

Around 8% to 14% of infants with a cow’s milk allergy will also react to soy. Babies with GI issues such as allergic proctocolitis or enterocolitis, conditions that cause inflammation in the GI tract, have a 25% to 60% chance of reacting to soy formulas.

Partially hydrolyzed formula. The milk proteins in partially hydrolyzed formula have been broken down into small pieces, but these pieces aren’t small enough not to trigger an allergic reaction in babies with a cow’s milk intolerance. This option isn’t hypoallergenic but is often labeled “gentle” for babies with easily upset tummies. It can be an option for babies with an intolerance to dairy.

Lactose-free formula. If your baby has signs of intolerance, the issue could be the sugar in the milk, lactose. Lactose-free formula is refined so that the lactose content is modified and replaced with a different form of sugar. 

Who Needs Hypoallergenic Formula?

Your doctor should diagnose a dairy allergy in your baby, but you may need to start hypoallergenic formula for your baby if they:

  • Have blood in their poop
  • Are constipated or have stools 
  • Aren’t gaining enough weight or meeting growth curves 
  • Often throw up after a feeding
  • Develop breathing problems
  • Get a rash after feeding

It may seem like an easier-to-digest option would be best for every baby, but studies also show that using these formulas doesn’t prevent the development of an allergy. The American Academy of Pediatrics recommends them only when medically necessary. 

Types of Hypoallergenic Formulas

All formulas are made of six basic parts:

  • Protein
  • Fat
  • Carbohydrates
  • Vitamins
  • Minerals
  • Other nutrients such as probiotics and prebiotics 

Different formula brands and types vary in their specific combinations of these ingredients. In cow’s milk formula, there are two types of proteins: casein and whey. In hypoallergenic formulas, these proteins are “pre-digested” in a chemical reaction with water, heat, or enzymes (hydrolyzed) so they are smaller. 

Other than the proteins being smaller, hypoallergenic formulas are the same, nutritionally, as standard formulas. Choices include:

Extensively hydrolyzed formula. The milk proteins in extensively hydrolyzed formula are broken down small enough that the body doesn’t recognize them as allergens. This is a great first option to try if your pediatrician has diagnosed your baby with a milk allergy.

Amino acid-based formula (elemental formula). This option breaks milk proteins down into their basic building blocks: amino acids. This option may be best for babies who have:

  • Anaphylactic reaction (trouble breathing, hives, low blood pressure, weak pulse) to milk proteins
  • Eosinophilic esophagitis, a condition that causes the buildup of white blood cells in the esophagus, which damages it and causes problems with swallowing
  • Severe rectal bleeding
  • Failure to thrive on other formulas

About 90% of babies with a cow’s milk allergy can tolerate extensively hydrolyzed formula or amino acid-based formula. 

What to Expect With Hypoallergenic Formula

The obvious pro to switching to hypoallergenic formula is that your baby can get the nutrition they need to grow and develop. But there are a few things you may notice after you switch:

  • Unusual smell and taste. If you’ve been using standard formula, you’ll notice a different odor to the formula powder. The taste can also be bitter, though most babies who drink it are too young to react to the difference. 
  • New look. Formula with broken-down proteins tends to look more watery and clearer in color after you mix it. This is normal.
  • Difference in the diaper. Your baby’s poop will look and smell different once they start on hypoallergenic formula. If your baby was having diarrhea on standard formula, you may see more solid stools. You may see more yellowish or green-colored stools, too. Be sure to report any black, white, or red poop to your doctor.
  • Expense. Because the creation of these special formulas takes more work, they’re pricey. If your baby needs hypoallergenic formula, check with your health insurance carrier. They may cover it as durable medical equipment (DME). 

Show Sources

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American Academy of Pediatrics: “Choosing a Baby Formula.”

FARE: “Milk Allergy Vs. Lactose Intolerance.”

Nutrition in Clinical Practice“What's in the Bottle? A Review of Infant Formulas.”

Kids With Food Allergies: “Formula Options for Kids with Food Allergies.”

Prevent Food Allergies: “Does My Baby Need Hypoallergenic Formula?”

Cleveland Clinic: “What’s the Right Baby Formula for My Newborn?”

Pediatrics: “The Effects of Early Nutritional Interventions on the Development of Atopic Disease in Infants and Children: The Role of Maternal Dietary Restriction, Breastfeeding, Hydrolyzed Formulas, and Timing of Introduction of Allergenic Complementary Foods.”

Medical Home Portal: “Formula Ingredients and Components.”

Nutrition Research and Practice: “A partially hydrolyzed whey formula provides adequate nutrition in high-risk infants for allergy.”

Mayo Clinic: “Anaphylaxis,” “Eosinophilic esophagitis.”