Autoinflammatory vs. Autoimmune: Dysfunction in Different Immune Systems

It’s all about innate and adaptive immunity

Autoimmune and autoinflammatory diseases all stem from problems in the immune system, but they’re differentiated by which part of the immune system is malfunctioning. In autoinflammation, it’s the innate immune system, while it’s the adaptive immune system that’s involved in autoimmunity. However, some diseases have aspects of both autoimmunity and autoinflammation.

In order to understand all of this, it helps to understand the innate and adaptive immune systems and how they act in these diseases. The immune system has two main functions: keep dangerous things out of your body, and attack and kill dangerous things that get in.

Illustration shows white blood cells being transported in the blood.


The Innate Immune System

Think of your body as a secure facility, and infectious agents as thieves trying to break in. Your innate immune system is the security that responds to an alarm and either keeps out or captures the intruders.

As the name suggests, the innate immune system is the one you’re born with. It’s your first line of defense, designed to recognize and defend you against broad categories of dangerous things: viruses, bacteria, fungi, parasites, and other potentially harmful particles. The innate immune system is part “keep it out” and part “attack and kill.”

To protect you from harm, the innate immune system uses:

  • Physical barriers: Skin and skin oils, body hair (such as eyelashes and nose hair), mucous membranes, and the respiratory and digestive tracts all present challenges to particles trying to make their way into your body.
  • Defense mechanisms: Some barriers are passive (like hair and skin), while others have active defense mechanisms, including mucus and tears that flush things out, sneezing and coughing that forcibly expel harmful substances, stomach acids that destroy them, and fevers that kill them off with heat.
  • General immune response: The body recognizes a foreign invader, tags invading cells for destruction, and begins destroying them.

Going deeper into the general immune response, once the body detects something that’s not part of you, it launches a response. A cascade of chemical signals goes out, telling the immune system that something got in and it needs to send help and mark invading cells as dangerous.

That help comes in the form of inflammation, which gets extra blood to carry a host of immune cells to the site. Your capillaries expand, causing the area to swell, and white blood cells called leukocytes rush in. These leukocytes immediately set out to consume and kill the invading cells.

You do have several types of leukocytes, including some that are specialized for bacteria, fungi, parasites, and allergens, and some that kill your cells that have become infected. The innate immune system’s response is immediate and works for, on average, about 96 hours (four days) before the adaptive immune system is ready to take over.

The Adaptive Immune System

When you hear about vaccines and how they teach your body to fight a particular pathogen, it’s the adaptive immune system that’s being discussed. This system learns and adapts as it encounters new intruders, devising specialized attacks for each specific pathogen it encounters.

So rather than attacking viruses in general, cells of the adaptive immune system—called antibodies—are highly specialized. An antibody created to attack the common cold can’t protect you from the flu or COVID-19. You need special antibodies for that. These are no mere security guards; these are snipers.

The cells involved in adaptive immunity are B-cells and T-cells. These cells don’t just hunt down and destroy specific invaders, they also remember them so they’re prepared for the next encounter. Vaccines introduce pathogens or parts of pathogens into your immune system to create this memory so your body knows what to do next time that pathogen invades your body.

Autoinflammatory Symptoms
  • Inflammation

  • Swollen lymph nodes

  • Rash

  • Recurrent fever

  • Chills

  • Body-wide inflammation that may cause symptoms based on affected organs and systems

Autoimmune Symptoms
  • Inflammation

  • Swollen lymph nodes

  • Rash

  • Recurrent low-grade fever

  • Pain

  • Fatigue

  • Difficulty concentrating

  • Symptoms specific to what’s being targeted

Autoinflammatory vs. Autoimmunity

Medical science recognized autoimmune diseases well before they did autoinflammatory diseases. In fact, autoinflammation is still much less recognized and understood than autoimmunity.

In autoimmune diseases, the adaptive immune system makes a mistake and determines that a cell type that’s actually “self” is “other.” It then forms autoantibodies to attack and destroy that type of cell. It may be a liver cell, a type of brain cell, a blood cell, or just about any type of cell in your body. 

More than 100 different autoimmune diseases have been identified, each with its own unique antibodies. The antibodies’ attack creates inflammation, damage, and pain. Beyond that, symptoms vary greatly depending on what type of tissue is under attack.

But some diseases with these symptoms, which were initially assumed to be autoimmune, don’t involve autoantibodies. The inflammation is there, but the adaptive immune system isn’t attacking. Instead, it appears that the innate immune system triggers the alarm, calling for the cascade of chemicals that lead to inflammation, and the alarm gets stuck. 

Research suggests that much of the time, this is due to genetics—the genes you’re born with—so these diseases run in families. However, some autoinflammatory diseases have been discovered that don’t appear to be directly inherited and instead may stem from somatic mutations—which take place during your lifetime—that affect innate immune cells.

The primary symptoms of autoinflammatory diseases are inflammation and fever, as those are part of the innate immune response. Systemic inflammation can cause numerous other symptoms, depending on where the inflammation is and which organs or systems it affects.

Disease Spectrum

While the mechanisms of autoinflammation and autoimmunity are different, they have a lot of overlapping symptoms, genetics, and physiological features. Some researchers have suggested that these diseases aren’t two separate things but rather opposite ends of a spectrum, with many diseases featuring a mix of innate and adaptive dysregulation.

Autoinflammatory-Autoimmune Disease Spectrum
Autoinflammatory  Autoimmune
TRAPS* Autoimmune lymphoproliferative syndrome
Crohn’s disease IPEX**
Gout Rheumatoid arthritis
Cryopyrin-associated periodic syndromes Type 1 diabetes
Deficiency of IL-1-receptor antagonist Sjogren’s syndrome 
Hyper IgD syndrome Lupus
*TNF receptor-associated periodic syndrome **Immunodysregulation polyendocrinopathy enteropathy X-linked syndrome


Autoimmune diseases involve the adaptive immune system, while autoinflammatory diseases involve the innate immune system.

A Word From Verywell

Autoinflammatory disease is still considered a new category, and the related illnesses aren’t well understood. You may even find healthcare workers who aren’t aware of this classification. While autoimmunity has been recognized for longer and researched considerably more, the medical community still has much to learn about it.

Ongoing research into both types of diseases and the immune system itself is likely to bring about a better understanding, increased awareness, better treatments, and possibly even preventive measures for these potentially debilitating conditions.

5 Sources
Verywell Health uses only high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial process to learn more about how we fact-check and keep our content accurate, reliable, and trustworthy.
  1. National Institutes of Health, U.S. National Library of Medicine: MedlinePlus. Immune response.

  2. Kaiser G. The Innate Immune System: An Overview. Cantonsville, Community College of Baltimore Country.

  3. American Autoimmune Related Diseases Association, Inc. There are more than 100 autoimmune diseases.

  4. Rheumatology Advisor. Autoinflammatory disorder.

  5. Arakelyan A, Nersisyan L, Poghosyan D, et al. Autoimmunity and autoinflammation: a systems view on signaling pathway dysregulation profiles. PLOS ONE. 2017;12(11):e0187572. doi:10.1371/journal.pone.0187572

Additional Reading

By Adrienne Dellwo
Adrienne Dellwo is an experienced journalist who was diagnosed with fibromyalgia and has written extensively on the topic.