IBD and Primary Immunodeficiency: What To Know

Medically reviewed by Ome Pérez-Gutiérrez, MD, AGAF
Written by Sherri Gordon, CLC
Posted on July 14, 2026

Key Takeaways

  • Inflammatory bowel disease (IBD) and primary immunodeficiency (PI) disorders can share surprisingly similar symptoms, including chronic diarrhea, abdominal pain, and malabsorption, making it important to understand how these two conditions connect.
  • View all takeaways

Inflammatory bowel disease (IBD) and primary immunodeficiency (PI) disorders can have surprisingly similar symptoms. Not only can both conditions cause digestive issues like chronic diarrhea, abdominal pain, and malabsorption, but they can also overlap or look like one another.

Understanding the connection between the two can empower you to ask the right questions about testing and treatments. Here’s what to know about the connection between IBD and PI, where symptoms may overlap, and how they may be treated.

Why Primary Immunodeficiency and IBD Can Overlap

Primary immunodeficiency — also called inborn errors of immunity (IEI) — is an inherited or acquired condition where the immune system doesn’t function like it should.

PI sometimes overlaps with IBD, a group of conditions including Crohn’s disease and ulcerative colitis that cause swelling and inflammation in the digestive tract.

When the genes involved in PI aren’t working properly, the intestinal lining may weaken and become inflamed. This can lead to symptoms that look very similar to those of IBD.

In fact, about one-third of people with PI have gut symptoms like gut inflammation, malabsorption, diarrhea, and pernicious anemia (a type of anemia caused by a weakened stomach lining). These issues arise because their gastrointestinal tract doesn’t have the necessary immune system cells.

Doctors sometimes call this group of symptoms IBD-like colitis. Most of the time, these symptoms show up in infants and children under age 6, but they can occur in adults.

Biggest Clues That IBD Symptoms May Be Tied to PI

If you have IBD-like symptoms that don’t seem to be getting better, or you’re experiencing frequent or unusual infections, it’s possible that your condition is tied to PI. Here are some of the biggest clues that your symptoms may be related to primary immunodeficiency.

Very Early Onset of Symptoms

About 15 percent of children diagnosed with IBD are diagnosed before they turn 6 years old, and up to 6 percent are diagnosed before they turn 3. Doctors call this condition very early onset IBD (VEO-IBD).

Some kids with very early onset IBD have specific genes associated with primary immunodeficiency disorders.

Kids with VEO-IBD tend to have more symptoms than those who are diagnosed when they’re older. Additionally, some of these kids have specific genes associated with primary immunodeficiency disorders, so some doctors recommend screening children with IBD for PI.

Delayed Growth or Slow Weight Gain

Kids who have VEO-IBD may have trouble gaining weight and growing normally, sometimes referred to as failure to thrive. They also may not meet developmental milestones.

Frequent or Unusual Infections

Unusual or recurrent infections could also be a clue that you may have a primary immunodeficiency disorder. In kids, signs might include:

  • Four or more ear infections in a year
  • Two or more sinus infections in a year
  • Two or more months of antibiotic treatment
  • Two or more bouts of pneumonia
  • Repeated deep skin abscesses
  • History of complex perianal abscesses from a very early age
  • Ongoing thrush
  • Need for IV antibiotics
  • Two or more systemic (bodywide) infections like septicemia (blood poisoning)

In adults, the signs may differ. Signs may include two or more ear infections in one year, two or more sinus infections in one year, one bout of pneumonia per year, and chronic diarrhea with weight loss. Repeated viral infections like herpes, warts, or condyloma could also be considered signs of PI.

Ineffectiveness of Standard IBD Treatments

If your IBD treatments don’t appear to be working or helping to improve your symptoms, you may want to ask your healthcare provider to run some tests. They can look for a connection between IBD and PI.

Some studies have found that those with very early onset IBD may be more resistant to conventional therapy for IBD. This doesn’t necessarily mean those with VEO-IBD have PI, but it could be worth investigating.

Family History

PI disorders result from genetic mutations (changes) that prevent your body’s immune system from working properly. Some of these changes appear randomly, but genetic mutations that lead to PI usually run in families.

Compared to people whose IBD presents later in life, people with VEO-IBD are more likely to have a family history of the condition. In fact, about 19 percent to 41 percent of people with VEO-IBD have a family history of IBD.

How Are People With IBD Evaluated for PI?

If you have IBD and your doctor thinks you may have PI, you will get blood tests to check how well your immune system is working. These tests may also show how your body has responded to vaccines. In some cases, your doctor may recommend genetic testing.

Getting the right diagnosis often takes teamwork. Your gastroenterologist, immunologist, and other specialists may need to work together.

Testing for PI often happens step by step instead of all at once. PI tests may include the following

Complete Blood Count

Many healthcare providers start with a complete blood count (CBC). This blood test checks the levels of different white blood cells, including lymphocytes, neutrophils, eosinophils, and monocytes. White blood cells help your body fight infections.

Serum Quantitative Immunoglobulins

This blood test measures your levels of immunoglobulins, such as IgG, IgA, and IgM. Immunoglobulins are proteins made by your immune system. They help your body find and fight germs. High or low levels can be a sign of an immune system disorder.

Vaccine Antibody Titers

Immunoglobulin levels can sometimes look normal even in people with PI. For this reason, healthcare providers may check antibody levels from vaccines you’ve had in the past. Antibodies are immune system proteins that help protect you from specific germs.

Getting the right diagnosis often takes teamwork. Your gastroenterologist, immunologist, and other specialists may need to work together.

If your antibody levels are low, your healthcare team may recommend a vaccine challenge. This means you receive a vaccine, then several weeks later your doctor checks whether your body made enough antibodies in response.

Lymphocyte Subset Analysis

This blood test looks more closely at lymphocytes, a type of white blood cell. It measures how many of these cells you have and whether the different types are in a healthy range.

When Is Genetic Testing Needed?

Genetic testing can be an important way to rule out or confirm a diagnosis of PI. For some people, it may also provide useful information that doctors can later use in developing a treatment plan.

In fact, one study found that treatment plans changed for 35 percent of people with PI who underwent genetic testing. But for some people, genetic testing may be too expensive. And it doesn’t guarantee insights for everyone. Talk to your healthcare team about whether genetic testing may be right for you.

Why Your Treatment Plan May Need To Change

If you have both IBD and PI, your healthcare team will need to find ways to balance your treatment to address both conditions in a safe way.

For instance, some medications used to manage IBD, like biologics, may suppress parts of your immune system. This can, in turn, increase your risk of infections. Your healthcare team will look for ways to manage your IBD without weakening your immune system.

Doctors sometimes recommend immunoglobulin replacement therapy for people with PI disorders to help prevent infections. This therapy provides antibodies collected from donated plasma. Your doctor will determine the best dosing schedule to minimize side effects.

You may also need individualized vaccine recommendations. Some vaccines are essential for preventing infections, while others may not be appropriate for your type of PI.

Likewise, the timing of your vaccines is also important when you have IBD, especially if you’re taking biologics or corticosteroids. Your healthcare team can let you know which vaccines you should get, when you should get them, and which you should avoid.

If you’re concerned your current treatment plan isn’t adequately addressing your IBD and PI, talk to your healthcare team. Together, you can decide the best way to improve your gut health and support your immune system.

Join the Conversation

On myPIteam, people share their experiences with primary immunodeficiency disorders, get advice, and find support from others who understand.

If you’ve been diagnosed with PI and IBD, what tips do you have for managing the two conditions? Let others know in the comments below.

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