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How Functional Medicine Treats More Than One Autoimmune Disease

October 22, 2025 by Dr. Tiffany Caplan, DC, CFMP, IFMCP & Dr. Brent Caplan, DC, CFMP, IFMCP

If you’ve been diagnosed with one autoimmune condition, you might wonder if you could
develop more than one autoimmune disease. The answer is yes. It’s not only possible, it’s
pretty common. We often see people at Caplan Health Institute who have multiple
autoimmune diseases. It’s called polyautoimmunity or polyautoimmune disease.

In the United States, polyautoimmune disease is as common as it is in our practice. A recent
study found that between January 2011 and January 2022, 15 million people were diagnosed
with at least one autoimmune disease and 34% of those people were diagnosed with more than
one autoimmune disease
. Specifically, 24% of the people had two autoimmune diseases, 8%
had three autoimmune diseases, and 2% had four or more autoimmune disorders.

This blog post will shed light on how to know if you have more than one autoimmune disease,
how to treat multiple autoimmune disorders, and why working with a functional medicine
provider can rebalance your immune system. The goal? Turn off the autoimmune process so
your body can heal.

Lupus + Rheumatoid Arthritis and Other Autoimmune Pairings

What kind of autoimmune diseases usually occur together? We’ve found that pretty much any
combination of autoimmune diseases can occur together, including lupus and rheumatoid
arthritis together. One of the most common combinations is when Hashimoto’s thyroiditis
occurs together with another autoimmune disease.

Hashimoto’s thyroiditis is an autoimmune disorder that affects the thyroid gland. A lot of times
conventional medical doctors don’t diagnose Hashimoto’s because they’re not checking for
thyroid problems in people who have autoimmune-related symptoms. So that diagnosis just
gets missed and overlooked.

Sjögren’s syndrome is another autoimmune disease that frequently occurs alongside other
autoimmune conditions. Statistics from the Sjögren’s Foundation show that about half the time,
Sjögren’s occurs along with autoimmune diseases like rheumatoid arthritis, lupus, or
scleroderma.

When to Suspect You May Have More Than One Autoimmune Disease

Figuring out whether you have more than one autoimmune disease can be tricky. A lot of the
symptoms of autoimmunity that people experience are general like fatigue, pain, and brain fog.
There’s a whole host of different conditions that can cause those problems or those symptoms.

So, figuring out if you have more than one autoimmune condition is not always easy with
symptoms alone. Here are some of the most common reasons we suspect multiple
autoimmune diseases at once:

  • If your doctor’s trying to address one autoimmune issue and you’re still having symptoms,
    that could be a sign that you’re battling more than one autoimmune disease.
  • Your symptoms are fluctuating a lot or presenting in different ways. For example, first you get
    flares of brain fog that switch to flares of skin rashes that are unexplained. That indicates there
    could be another autoimmune process happening in a different part of your body.
  • Having a really strong family history of different autoimmune conditions. Let’s say you get
    diagnosed with multiple sclerosis (MS), but a lot of people in your family are also taking thyroid
    medication. This could be a sign that you may also have Hashimoto’s on top of the MS.
  • A positive Antinuclear Antibody Test (ANA). This blood test checks for the presence of
    antinuclear antibodies. Antibodies are proteins your immune system makes to fight invaders
    like viruses or bacteria. However, antinuclear antibodies mistakenly go after your body’s own
    cells, indicating the presence of autoimmune disease. A positive ANA result could be a sign that
    there are some things going on systemically with the immune system, causing potential for
    multiple different types of tissues to be the target of the antibodies.

Diagnosing Polyautoimmune Disease

At Caplan Health Institute, we don’t spend a lot of time figuring out exactly what autoimmune
labels you have. That’s because the root causes are often the same and the treatments are the
same, regardless of which autoimmune disorders you have.

This is a fundamental difference in how conventional medicine approaches autoimmune
disease compared to functional medicine.

In conventional medicine, there is a strong emphasis on the diagnosis. Once a practitioner has
the diagnosis, he/she/they can then prescribe the appropriate medication for the symptoms.
Conventional medicine providers rarely consider root causes or know how to address them. If
the lab results don’t clearly show an identifiable autoimmune disease, they just wait. Patients
don’t get answers until the autoimmune disease -and their lab results- get worse.

The functional medicine approach is to address the root causes of the immune system
dysfunction, not the symptoms. In this way we can turn off, slow down, or even reverse
autoimmune diseases. In our experience, the best way to approach it is by looking at what’s causing the immune system to attack different tissues of the body. That’s why we don’t usually
order a lot of diagnostic labeling tests for polyautoimmunity.

It’s not even necessary to really get that label as long as we can support the immune system
back to better function. Supporting immunity is the whole goal. We could do a lot more testing,
but it’s never going to make that big of a difference in how we treat polyautoimmunity.

A lot of times, when I’m meeting people for the first time, they’re like, “I need a diagnosis.” I
ask them right off the bat, what’s the diagnosis really going to necessarily get you, except
maybe give you peace of mind that you’re not crazy?

We do some basic tests to figure out the root causes of a person’s autoimmune issues. But we
don’t want you to end up spending a whole bunch of money and time doing all these different
tests just to be able to put a name on your autoimmune condition/s, without getting any
clinically useful information.

Polyautoimmune Disease: the Functional Medicine Approach

In conventional medicine, when somebody has multiple autoimmune diseases they are looked
at as separate issues. The person is given a team of different specialists. Depending on the
diagnosis, a person might see a rheumatologist, an endocrinologist, a gastroenterologist, a
dermatologist or other specialist. But when we look at it from a functional medicine
perspective, all these autoimmune disorders are connected from the root because it’s the
immune system causing problems.

With polyautoimmunity, functional medicine is really going to be the best way to connect all of
the dots. It addresses all of these different conditions at the same time from the root, instead
of trying to separately address all the symptoms. If your immune system is imbalanced and
attacking your own tissues, we have to find what’s causing the immune system to act
abnormally. If that’s not identified and resolved, then there’s nothing to stop the immune
system from attacking more tissues or causing other types of damage in the body. The reason
why people develop multiple autoimmune diseases is because the root problems of their
immune system dysfunction have not been addressed. We need to find the common
denominator of what’s causing the immune system to attack different tissues.

We summarize these in one of our most popular blog posts, “Nine Root Causes of Autoimmune
Disorders.”

Treating Multiple Autoimmune Diseases

The good news is that taking a functional medicine approach and realizing that all your
autoimmune diseases are connected really simplifies the process. Instead of looking at it as five
different conditions that you have to treat separately, you’re really just trying to piece it
together and figure out what are the common denominators between those conditions.

When we are looking at it from a root-cause perspective, we’re not just looking at what’s
caused one autoimmune disease; we’re really looking at what are the underlying causes that
set up for developing multiple autoimmune disorders. The goal is to treat the common
denominators between those conditions, which usually include:

  • Diet – Dietary changes can help all autoimmune diseases. Whether somebody has a thyroid
    issue or they have celiac or they have rheumatoid arthritis or psoriasis, making the right dietary
    changes for those people makes a difference. If people have food sensitivities or intolerances,
    they can react to certain foods, which puts the immune system into a state of inflammation or
    irritation. We make sure they’re getting the right nutrition and that they’re eating safe foods
    (that their immune system is not reacting to) by trying an elimination diet or rotation diet and
    personalizing it to each person. Our microbes eat the same foods we eat. So, balancing the
    microbiome with the right foods helps to restore a healthy immune system.
  • Lifestyle – How do we help someone address autoimmune disease root causes through
    lifestyle habits? That could mean improving how they cope with stress, their sleep, or their
    exercise or mental emotional health. Those things all affect how the immune system works.

If you have multiple autoimmune diseases, the medical information you are given can be
depressing. Conventional medicine presents autoimmune disease as an incurable disease that
you’re going to have forever. They say the best you can hope for is symptom management. So
now you’re thinking: I have multiple autoimmune diseases. This is terrible, right? Wrong.

There is hope, even for somebody who has five autoimmune diseases, because it’s really no
different than when we’re working with somebody who has only one autoimmune disease. It
doesn’t make any difference because we’re treating the causes of the immune problems all at
the same time instead of trying to just band-aid each thing separately.

The good news is that it doesn’t make it necessarily any more complicated. On our end as
clinicians, we have to be aware of the little nuances of each condition, so that we make sure
we’re not making anything worse in the process. But from the patient perspective, the
treatment protocol is the same. Your job toward healing autoimmune disease isn’t any more
difficult.

Tackling More Than One Autoimmune Disease

The best way to treat polyautoimmune disease is to work with a functional medicine provider.
At Caplan Health Institute, we can dig down to the root causes of your multiple autoimmune
diseases.

The first step? Schedule a free 15-minute discovery consultation, by phone or video.

If you decide to come on board as a practice member, we can take a complete medical history
and then personalize your treatment plan. We call our patients “practice members” because
they take an active role in their health. In addition, our Caplan Health Institute coaches can
work with you to make sure you’re sticking with the plan. The goal is to eliminate anything that is dragging down your immune system and build up your immune system with what it needs to
operate effectively. You’ll conquer your polyautoimmunity and feel like your old self again.

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