Your child’s ‘second brain:’ the brain-gut connection, explained

Close-up of a child curled up on a couch

Every parent has wondered, “Why is my child’s stomach hurting? Is there something seriously wrong? How can I help them feel better?”

Abdominal pain is one of the most common childhood complaints, and a very real stressor. Most the time, chronic abdominal pain happens in a healthy child whose gastrointestinal (GI) tract – the esophagus, stomach and intestines – is working well.

The GI tract is full of nerves – so many that it is called the “second brain.” Nerves allow us to move and feel sensations in our body. The nerves in your GI tract are constantly communicating with the brain in your head – the brain-gut connection. If you’ve ever had a “gut feeling” or butterflies in your stomach, you have experienced this brain-gut connection.

What is functional abdominal pain?

The GI tract is busy with many important jobs, like absorbing nutrients and eliminating waste. Usually our brains can ignore what our GI tract is working on. Sometimes signals from the nerves get confused, and the usual work of the GI tract is perceived by the brain as pain or discomfort. This is called “functional abdominal pain.” Irritable bowel syndrome is a type of functional abdominal pain that includes diarrhea or constipation.

Why does functional abdominal pain happen?

Humans are designed to pay close attention to pain in order to keep our bodies safe and healthy. It’s important to feel pain if we touch a hot stove or break a bone, so we can address the problem and avoid further harm.

In functional abdominal pain, the nerves send pain signals to our brain even though there’s no harm or damage in the GI tract. Functional pain is like a car alarm that’s set off by the wind: the alarm is there to protect the car, but it is triggered by something harmless, so it’s a false alarm.

This kind of abdominal pain is like a headache. The vast majority of the time when we have headaches, there’s no damage or injury in the brain – the pain is real, but the brain is healthy.

Different things can change the nerve signals in a healthy GI tract, causing functional abdominal pain. Some examples are a previous infection, genes, diet, stress and our gut microbiome (the bacteria living in our intestines).

How is functional abdominal pain diagnosed?

Your child doesn’t need a specific test to be diagnosed with functional abdominal pain. Healthcare providers can often diagnose it based on symptoms and physical exam. Tests for other causes of chronic abdominal pain may be needed if your child isn’t growing normally or has other signs that concern your provider.

How is functional abdominal pain treated?

For some kids, medicines or a healthier diet – a greater variety of whole foods including vegetables and fruits, and fewer processed sweets and greasy foods – may be helpful. Since the nerve signals from the GI tract are processed in the brain, the most effective treatments for functional abdominal pain actually target the brain, decreasing pain through the brain-gut connection.

It’s stressful to be in pain, especially when chronic or frequent. A psychologist or counselor can teach kids ways to cope with pain, such as relaxation techniques (e.g., diaphragmatic breathing, guided imagery) and teaching their brains find more helpful ways to think about pain. Children with functional abdominal pain do best when they continue to participate in school and other activities – to the extent that is safe and possible in the setting of the COVID-19 pandemic – and get regular exercise and quality sleep.

Functional abdominal pain is the most common cause for chronic belly pain in kids. Because the GI tract is the second brain, children have a powerful and effective tool to manage this pain – the brains in their head!


Amanda Lee, M.D.Headshot of a smiling woman
Assistant Professor of Pediatrics
Division of Gastroenterology
OHSU Doernbecher Children’s Hospital

Professional headshot of a smiling womanJacklyn Stellway, Psy.D.
Assistant Professor of Pediatrics
Divisions of Gastroenterology and Psychology
OHSU Doernbecher Children’s Hospital