Your baby may pass mucus in their stool as part of the natural digestive process. But certain health conditions can also cause mucus in their poop.

Because their diet is liquid in the first months of life, a baby has stool that doesn’t resemble an older child’s or adult’s. Sometimes it’s hard to know if your baby’s stool is normal in appearance or something to call the doctor about.

One example is the presence of mucus. Sometimes the mucus is part of a normal process. Other times, it can be a sign of an underlying infection or medical condition.

Read on to learn when a parent should be concerned about mucus in baby poop.

What are the causes of mucus in baby poop?

Mucus in baby poop isn’t always cause for concern. The intestines naturally secrete mucus to help stool pass more effectively through the intestines.

Sometimes, a baby may pass some of this mucus in their stool without any underlying condition. The mucus can look like slimy streaks or strings. Sometimes the mucus is jelly-like in appearance.

Babies who are breastfed may be more likely to have mucus in their poop because their stool passes through their intestines relatively quickly.

However, sometimes there are medical conditions that can cause mucus in stool, including infections, allergies, and more.


A bacterial or viral infection (stomach flu) can irritate the intestines and lead to inflammation. The result is increased mucus in baby’s poop.

Additional symptoms that could indicate infection include fever and irritability. Babies with an infection may also have green stool. Some blood may even be present in cases of extreme irritation.

With a bacterial infection, there is often blood in the stool along with mucus.

Food allergy

Food allergies can cause inflammation. Inflammation causes increased mucus secretion, which leads to more mucus in a baby’s stool. These symptoms will usually appear within a baby’s first two months of life. Signs a baby may have a food allergy include:

  • being fussy and hard to console
  • vomiting
  • bloody stool


Teething babies aren’t only cranky — symptoms may include mucus in their stool. The presence of excess saliva and the pain from teething can irritate the intestines, resulting in excess mucus in the stool.

Cystic fibrosis

Babies with cystic fibrosis may have increased amounts of mucus as a side effect of this condition. The mucus tends to be foul-smelling and greasy in appearance. A child may also have poor weight gain and delayed growth related to cystic fibrosis.

The condition also causes excess mucus to develop in organs, especially the lungs, pancreas, liver, and intestines.

Because cystic fibrosis can interfere with a child’s digestion, a doctor may recommend specific enzymes for treatment. If a baby’s weight gain is very poor, sometimes a feeding tube is used to provide nutrition.


Intussusception is a serious medical condition that can occur when an infant’s intestines slide into each other, a process known as “telescoping.” This is a medical emergency because blood flow is lost to the intestine and stool becomes blocked.

As a result, a baby may only be able to pass mucus that has been excreted below the blocked area. The stool often resembles dark red jelly. Other symptoms of intussusception include:

  • abdominal pain that comes and goes
  • vomiting
  • blood in the stool
  • lethargy or extreme sleepiness

When should you see a doctor about mucus in baby poop?

The condition isn’t usually cause for concern as long as your baby is behaving normally and doesn’t have any signs of infection or illness, such as:

  • inconsolable fussiness
  • fever
  • blood in the stool

If there are signs of infection or illness along with mucus in the baby’s poop, you should contact your child’s doctor.

Also contact your child’s doctor if your baby is refusing fluids or drinking minimal fluids and starts to appear dehydrated. Signs of dehydration include not crying tears or having few wet diapers.

You should continue to monitor your child’s stool. If your baby is continually having stool that contains mucus and you’re concerned, contact your child’s pediatrician.

If you notice red, bloodlike tinges in your baby’s poop or your baby is acting ill for no known reason, call your child’s doctor. The doctor can direct a parent to the emergency room if necessary.

What are the treatments for mucus in baby poop?

Treatments for mucus in baby’s poop depends on the underlying cause.

For example, a doctor would recommend supportive treatment for a baby with a viral stomach infection. This can include fluids to prevent dehydration and medications to keep fever down.

If allergies are the underlying cause of mucus in baby poop, a doctor may recommend an elimination diet for the mom if she is breastfeeding. Examples include eliminating cow’s milk from your diet.

If a baby is formula-fed, a doctor may recommend switching formulas to a milk-free (also called “elemental”) option.

If intussusception is the underlying cause of mucus in baby poop, a doctor will likely recommend surgery to correct the intestinal overlap. In some instances, they may be able to use a barium or air enema to promote the “straightening out” of the intestines.

Whatever the approach to intussusception, prompt treatment is vital to prevent loss of blood flow to the intestines. Otherwise, an infant is at greater risk for bowel perforation (hole in the intestine).

What is the outlook?

In most instances, mucus in baby poop isn’t a cause for concern. It can be a normal by-product of digestion, especially given the fast digestion that babies usually have.

Parents are likely to notice that a baby has mucus in stool one day, then doesn’t on another. The symptoms will likely go away as a baby gets older and solid foods are introduced. At this time, stool starts to become more formed.

However, if a baby is acting ill, has blood in their stool, or is having prolonged poor feeding episodes, a parent should seek medical attention for their little one.